From b512be51a9c79daa420b3be8905f8a47140a2966 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Tue, 27 Aug 2024 10:31:57 +0200
Subject: [PATCH 01/24] Bump versions

---
 CHANGELOG.md              | 12 ++++++++++++
 assets/multiqc_config.yml |  4 ++--
 nextflow.config           |  2 +-
 3 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6089039e..18ddc29e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,18 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## dev [unreleased]
+
+### `Added`
+
+### `Changed`
+
+### `Fixed`
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## 3.0.3 [2024-08-27]
 
 ### `Added`
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 10c24150..9f4e5e7e 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/3.0.3" target="_blank">nf-core/mag</a>
+  This report has been generated by the <a href="https://github.com/nf-core/mag/tree/dev" target="_blank">nf-core/mag</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/mag/3.0.3/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/mag/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-mag-methods-description":
     order: -1000
diff --git a/nextflow.config b/nextflow.config
index 9306ae99..85be4905 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -390,7 +390,7 @@ manifest {
     description     = """Assembly, binning and annotation of metagenomes"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '3.0.3'
+    version         = '3.0.4dev'
     doi             = '10.1093/nargab/lqac007'
 }
 

From df026135c66f207d1a139ccb3501ddcfc1631867 Mon Sep 17 00:00:00 2001
From: "Diego Alvarez S." <dialvarezs@gmail.com>
Date: Sun, 8 Sep 2024 04:09:13 -0300
Subject: [PATCH 02/24] Update GTDBTk to v2.4.0

---
 bin/summary_gtdbtk.py                             | 10 +++++-----
 modules.json                                      |  2 +-
 modules/nf-core/gtdbtk/classifywf/environment.yml |  4 +---
 modules/nf-core/gtdbtk/classifywf/main.nf         |  4 ++--
 4 files changed, 9 insertions(+), 11 deletions(-)

diff --git a/bin/summary_gtdbtk.py b/bin/summary_gtdbtk.py
index 7ae43a09..370ea4fa 100755
--- a/bin/summary_gtdbtk.py
+++ b/bin/summary_gtdbtk.py
@@ -76,11 +76,11 @@ def main(args=None):
     columns = [
         "user_genome",
         "classification",
-        "fastani_reference",
-        "fastani_reference_radius",
-        "fastani_taxonomy",
-        "fastani_ani",
-        "fastani_af",
+        "closest_genome_reference",
+        "closest_genome_reference_radius",
+        "closest_genome_taxonomy",
+        "closest_genome_ani",
+        "closest_genome_af",
         "closest_placement_reference",
         "closest_placement_radius",
         "closest_placement_taxonomy",
diff --git a/modules.json b/modules.json
index 0cab4e4e..b17f7dc3 100644
--- a/modules.json
+++ b/modules.json
@@ -124,7 +124,7 @@
                     },
                     "gtdbtk/classifywf": {
                         "branch": "master",
-                        "git_sha": "0735b6d2b509cbb5cf71d15fda819cd7392722fe",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
                         "installed_by": ["modules"]
                     },
                     "gunc/downloaddb": {
diff --git a/modules/nf-core/gtdbtk/classifywf/environment.yml b/modules/nf-core/gtdbtk/classifywf/environment.yml
index 8801269e..500531ea 100644
--- a/modules/nf-core/gtdbtk/classifywf/environment.yml
+++ b/modules/nf-core/gtdbtk/classifywf/environment.yml
@@ -1,7 +1,5 @@
-name: gtdbtk_classifywf
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::gtdbtk=2.3.2
+  - bioconda::gtdbtk=2.4.0
diff --git a/modules/nf-core/gtdbtk/classifywf/main.nf b/modules/nf-core/gtdbtk/classifywf/main.nf
index 14dd28a4..9fc7a32d 100644
--- a/modules/nf-core/gtdbtk/classifywf/main.nf
+++ b/modules/nf-core/gtdbtk/classifywf/main.nf
@@ -5,8 +5,8 @@ process GTDBTK_CLASSIFYWF {
     // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gtdbtk:2.3.2--pyhdfd78af_0' :
-        'biocontainers/gtdbtk:2.3.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gtdbtk:2.4.0--pyhdfd78af_1' :
+        'biocontainers/gtdbtk:2.4.0--pyhdfd78af_1' }"
 
     input:
     tuple val(meta), path("bins/*")

From e4fa8a9822b697b181c5840cb74a739baf748402 Mon Sep 17 00:00:00 2001
From: "Diego Alvarez S." <dialvarezs@gmail.com>
Date: Sun, 8 Sep 2024 04:22:06 -0300
Subject: [PATCH 03/24] Changelog

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 18ddc29e..e12b47a5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Dependencies`
 
+| Tool     | Previous version | New version |
+| -------- | ---------------- | ----------- |
+| GTDBTk   | 2.3.2            | 2.4.0       |
+
 ### `Deprecated`
 
 ## 3.0.3 [2024-08-27]

From 55803753f4774fac127c2ef129b7b33dd1d28e68 Mon Sep 17 00:00:00 2001
From: "Diego Alvarez S." <dialvarezs@gmail.com>
Date: Sun, 8 Sep 2024 04:36:19 -0300
Subject: [PATCH 04/24] Prettier

---
 CHANGELOG.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e12b47a5..d056eefa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,9 +13,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Dependencies`
 
-| Tool     | Previous version | New version |
-| -------- | ---------------- | ----------- |
-| GTDBTk   | 2.3.2            | 2.4.0       |
+| Tool   | Previous version | New version |
+| ------ | ---------------- | ----------- |
+| GTDBTk | 2.3.2            | 2.4.0       |
 
 ### `Deprecated`
 

From 080eac6108f8fd7b642635af8966ad4f06480aff Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Mon, 9 Sep 2024 08:57:16 +0000
Subject: [PATCH 05/24] Bump GTDB release version, better changelog

---
 CHANGELOG.md          | 2 ++
 conf/test_full.config | 2 +-
 nextflow.config       | 2 +-
 nextflow_schema.json  | 2 +-
 4 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d056eefa..63515e3f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- [#664](https://github.com/nf-core/mag/pull/664) - Update GTDBTk to latest version, with updated column names, update GTDB to release 220 (by @dialvarezs)
+
 ### `Fixed`
 
 ### `Dependencies`
diff --git a/conf/test_full.config b/conf/test_full.config
index d7f3365e..9a01bc58 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -22,7 +22,7 @@ params {
     //centrifuge_db = "s3://ngi-igenomes/test-data/mag/p_compressed+h+v.tar.gz"
     kraken2_db    = "s3://ngi-igenomes/test-data/mag/minikraken_8GB_202003.tgz"
     cat_db        = "s3://ngi-igenomes/test-data/mag/CAT_prepare_20210107.tar.gz"
-    // gtdb_db       = "s3://ngi-igenomes/test-data/mag/gtdbtk_r214_data.tar.gz"
+    // gtdb_db       = "s3://ngi-igenomes/test-data/mag/gtdbtk_r214_data.tar.gz" ## This should be updated to release 220, once we get GTDB-Tk working again
     skip_gtdbtk   = true
 
     // TODO TEMPORARY: deactivate SPAdes due to incompatibility of container with fusion file system
diff --git a/nextflow.config b/nextflow.config
index 85be4905..8338e9f3 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -87,7 +87,7 @@ params {
     cat_official_taxonomy                = false
     save_cat_db                          = false
     skip_gtdbtk                          = false
-    gtdb_db                              = "https://data.ace.uq.edu.au/public/gtdb/data/releases/release214/214.1/auxillary_files/gtdbtk_r214_data.tar.gz"
+    gtdb_db                              = "https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r220_data.tar.gz"
     gtdb_mash                            = null
     gtdbtk_min_completeness              = 50.0
     gtdbtk_max_contamination             = 10.0
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 35e85825..219d6724 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -537,7 +537,7 @@
                 "gtdb_db": {
                     "type": "string",
                     "description": "Specify the location of a GTDBTK database. Can be either an uncompressed directory or a `.tar.gz` archive. If not specified will be downloaded for you when GTDBTK or binning QC is not skipped.",
-                    "default": "https://data.ace.uq.edu.au/public/gtdb/data/releases/release214/214.1/auxillary_files/gtdbtk_r214_data.tar.gz"
+                    "default": "https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/auxillary_files/gtdbtk_package/full_package/gtdbtk_r220_data.tar.gz"
                 },
                 "gtdb_mash": {
                     "type": "string",

From f11d9ae34e31819cb06542ca54b39bbeafada472 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Mon, 9 Sep 2024 13:51:38 +0000
Subject: [PATCH 06/24] Add support for pre-supplying bowtie2 host index

---
 CHANGELOG.md                           |  2 ++
 modules/local/bowtie2_removal_align.nf |  6 +++++-
 modules/local/bowtie2_removal_build.nf |  6 +++---
 nextflow.config                        |  1 +
 nextflow_schema.json                   |  5 +++++
 workflows/mag.nf                       | 14 ++++++++++----
 6 files changed, 26 insertions(+), 8 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 18ddc29e..803adad7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#665](https://github.com/nf-core/mag/pull/648) - Add support for supplying pre-made bowtie host reference index (requested by @simone-pignotti, added by @jfy133)
+
 ### `Changed`
 
 ### `Fixed`
diff --git a/modules/local/bowtie2_removal_align.nf b/modules/local/bowtie2_removal_align.nf
index 03cb9b25..79eb0e47 100644
--- a/modules/local/bowtie2_removal_align.nf
+++ b/modules/local/bowtie2_removal_align.nf
@@ -26,8 +26,12 @@ process BOWTIE2_REMOVAL_ALIGN {
     def save_ids = (args2.contains('--host_removal_save_ids')) ? "Y" : "N"
     if (!meta.single_end){
         """
+        INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/\\.rev.1.bt2\$//"`
+        [ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/\\.rev.1.bt2l\$//"`
+        [ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1
+
         bowtie2 -p ${task.cpus} \
-                -x ${index[0].getSimpleName()} \
+                -x \$INDEX \
                 -1 "${reads[0]}" -2 "${reads[1]}" \
                 $args \
                 --un-conc-gz ${prefix}.unmapped_%.fastq.gz \
diff --git a/modules/local/bowtie2_removal_build.nf b/modules/local/bowtie2_removal_build.nf
index ba152611..f3922094 100644
--- a/modules/local/bowtie2_removal_build.nf
+++ b/modules/local/bowtie2_removal_build.nf
@@ -10,14 +10,14 @@ process BOWTIE2_REMOVAL_BUILD {
     path fasta
 
     output:
-    path 'bt2_index_base*', emit: index
-    path "versions.yml"   , emit: versions
+    path "*.bt2"        , emit: index
+    path "versions.yml" , emit: versions
 
     script:
     def args = task.ext.args ?: ''
     """
     mkdir bowtie
-    bowtie2-build --threads $task.cpus $fasta "bt2_index_base"
+    bowtie2-build --threads $task.cpus $fasta ${fasta.simpleName}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/nextflow.config b/nextflow.config
index 85be4905..aa0ef836 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -31,6 +31,7 @@ params {
     phix_reference                       = "${baseDir}/assets/data/GCA_002596845.1_ASM259684v1_genomic.fna.gz"
     save_phixremoved_reads               = false
     host_fasta                           = null
+    host_fasta_bowtie2index              = null
     host_genome                          = null
     host_removal_verysensitive           = false
     host_removal_save_ids                = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 35e85825..f8064be5 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -383,6 +383,11 @@
                     "description": "Fasta reference file for host contamination removal.",
                     "help_text": "This parameter is mutually exclusive with `--host_genome`. The reference can be masked. Host read removal is done with Bowtie2."
                 },
+                "host_fasta_bowtie2index": {
+                    "type": "string",
+                    "description": "Bowtie2 index directory corresponding to --host_fasta reference file for host contamination removal.",
+                    "help_text": "This parameter must be used in combination with --host_fasta, and should be a directory containing files from the output of `bowtie2-build`, i.e. files ending in `.bt2`"
+                },
                 "host_removal_verysensitive": {
                     "type": "boolean",
                     "description": "Use the `--very-sensitive` instead of the`--sensitive`setting for Bowtie 2 to map reads against the host genome."
diff --git a/workflows/mag.nf b/workflows/mag.nf
index f71d4218..6c158284 100644
--- a/workflows/mag.nf
+++ b/workflows/mag.nf
@@ -250,11 +250,17 @@ workflow MAG {
         }
 
         if (params.host_fasta){
-            BOWTIE2_HOST_REMOVAL_BUILD (
-                ch_host_fasta
-            )
-            ch_host_bowtie2index = BOWTIE2_HOST_REMOVAL_BUILD.out.index
+            if ( params.host_fasta_bowtie2index ) {
+                ch_host_bowtie2index = file(params.host_fasta_bowtie2index, checkIfExists: true)
+            } else {
+                BOWTIE2_HOST_REMOVAL_BUILD (
+                    ch_host_fasta
+                )
+                ch_host_bowtie2index = BOWTIE2_HOST_REMOVAL_BUILD.out.index
+            }
+
         }
+
         ch_bowtie2_removal_host_multiqc = Channel.empty()
         if (params.host_fasta || params.host_genome){
             BOWTIE2_HOST_REMOVAL_ALIGN (

From ca8ba9d08701acf55dfcbc2dec2c0e1e535d4bd9 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 11 Sep 2024 05:17:42 +0200
Subject: [PATCH 07/24] Improve condition so SPLIT_FASTQ skipped if only
 concoct selected as binner

---
 CHANGELOG.md                  |  2 ++
 subworkflows/local/binning.nf | 12 +++++++-----
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 1c2c8c05..08c3c625 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#667](https://github.com/nf-core/mag/pull/667) - Fix pipeline crashing if only CONCOCT selected during binning (reported and fixed by @jfy133)
+
 ### `Dependencies`
 
 | Tool   | Previous version | New version |
diff --git a/subworkflows/local/binning.nf b/subworkflows/local/binning.nf
index a07ca416..83f0f38e 100644
--- a/subworkflows/local/binning.nf
+++ b/subworkflows/local/binning.nf
@@ -94,7 +94,7 @@ workflow BINNING {
                                     bams: [ meta, bams, bais ]
                             }
 
-        FASTA_BINNING_CONCOCT ( ch_concoct_input )
+        FASTA_BINNING_CONCOCT ( ch_concoct_input.bins, ch_concoct_input.bams )
         ch_final_bins_for_gunzip = ch_final_bins_for_gunzip.mix( FASTA_BINNING_CONCOCT.out.bins.transpose() )
         ch_binning_results_gzipped_final = ch_binning_results_gzipped_final.mix( FASTA_BINNING_CONCOCT.out.bins )
         ch_versions = ch_versions.mix(FASTA_BINNING_CONCOCT.out.versions)
@@ -102,10 +102,12 @@ workflow BINNING {
 
     // decide which unbinned fasta files to further filter, depending on which binners selected
     // NOTE: CONCOCT does not produce 'unbins' itself, therefore not included here.
-    if ( !params.skip_metabat2 & params.skip_maxbin2 ) {
+    if ( !params.skip_metabat2 && params.skip_maxbin2 ) {
         ch_input_splitfasta = METABAT2_METABAT2.out.unbinned
-    } else if ( params.skip_metabat2 & !params.skip_maxbin2 ) {
+    } else if ( params.skip_metabat2 && !params.skip_maxbin2 ) {
         ch_input_splitfasta = MAXBIN2.out.unbinned_fasta
+    } else if ( params.skip_metabat2 && params.skip_maxbin2 ) {
+        ch_input_splitfasta = Channel.empty()
     } else {
         ch_input_splitfasta = METABAT2_METABAT2.out.unbinned.mix(MAXBIN2.out.unbinned_fasta)
     }
@@ -116,11 +118,11 @@ workflow BINNING {
     ch_split_fasta_results_transposed = SPLIT_FASTA.out.unbinned.transpose()
     ch_versions = ch_versions.mix(SPLIT_FASTA.out.versions)
 
-    GUNZIP_BINS ( ch_final_bins_for_gunzip )
+    GUNZIP_BINS ( ch_final_bins_for_gunzip.dump(tag: 'final_bins') )
     ch_binning_results_gunzipped = GUNZIP_BINS.out.gunzip
         .groupTuple(by: 0)
 
-    GUNZIP_UNBINS ( ch_split_fasta_results_transposed )
+    GUNZIP_UNBINS ( ch_split_fasta_results_transposed.dump(tag: 'final_unbins') )
     ch_splitfasta_results_gunzipped = GUNZIP_UNBINS.out.gunzip
         .groupTuple(by: 0)
 

From 9fc4153e254b6a0a9f4b804d4d394d756754379c Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Thu, 12 Sep 2024 19:20:37 +0200
Subject: [PATCH 08/24] Update subworkflows/local/binning.nf

---
 subworkflows/local/binning.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/binning.nf b/subworkflows/local/binning.nf
index 83f0f38e..6985f82e 100644
--- a/subworkflows/local/binning.nf
+++ b/subworkflows/local/binning.nf
@@ -118,7 +118,7 @@ workflow BINNING {
     ch_split_fasta_results_transposed = SPLIT_FASTA.out.unbinned.transpose()
     ch_versions = ch_versions.mix(SPLIT_FASTA.out.versions)
 
-    GUNZIP_BINS ( ch_final_bins_for_gunzip.dump(tag: 'final_bins') )
+    GUNZIP_BINS ( ch_final_bins_for_gunzip )
     ch_binning_results_gunzipped = GUNZIP_BINS.out.gunzip
         .groupTuple(by: 0)
 

From fcdb5184013f7a1665dd0fa0e706fb637e582996 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Thu, 12 Sep 2024 19:20:43 +0200
Subject: [PATCH 09/24] Update subworkflows/local/binning.nf

---
 subworkflows/local/binning.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/binning.nf b/subworkflows/local/binning.nf
index 6985f82e..51caaeb9 100644
--- a/subworkflows/local/binning.nf
+++ b/subworkflows/local/binning.nf
@@ -122,7 +122,7 @@ workflow BINNING {
     ch_binning_results_gunzipped = GUNZIP_BINS.out.gunzip
         .groupTuple(by: 0)
 
-    GUNZIP_UNBINS ( ch_split_fasta_results_transposed.dump(tag: 'final_unbins') )
+    GUNZIP_UNBINS ( ch_split_fasta_results_transposed )
     ch_splitfasta_results_gunzipped = GUNZIP_UNBINS.out.gunzip
         .groupTuple(by: 0)
 

From 9d9e4eda432f18d1b8175fb6116ec12b8eb213d7 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Fri, 13 Sep 2024 16:08:39 +0200
Subject: [PATCH 10/24] Fix module failure when no bins

---
 modules.json                              |  2 +-
 modules/nf-core/gtdbtk/classifywf/main.nf | 55 +++++++++++------------
 2 files changed, 27 insertions(+), 30 deletions(-)

diff --git a/modules.json b/modules.json
index b17f7dc3..64207e26 100644
--- a/modules.json
+++ b/modules.json
@@ -124,7 +124,7 @@
                     },
                     "gtdbtk/classifywf": {
                         "branch": "master",
-                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "git_sha": "c44b5e99aea273adf455d8c40babeb3885083ff9",
                         "installed_by": ["modules"]
                     },
                     "gunc/downloaddb": {
diff --git a/modules/nf-core/gtdbtk/classifywf/main.nf b/modules/nf-core/gtdbtk/classifywf/main.nf
index 9fc7a32d..9aa13ee4 100644
--- a/modules/nf-core/gtdbtk/classifywf/main.nf
+++ b/modules/nf-core/gtdbtk/classifywf/main.nf
@@ -1,29 +1,25 @@
 process GTDBTK_CLASSIFYWF {
     tag "${prefix}"
     label 'process_medium'
-
-    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gtdbtk:2.4.0--pyhdfd78af_1' :
-        'biocontainers/gtdbtk:2.4.0--pyhdfd78af_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gtdbtk:2.4.0--pyhdfd78af_1' : 'biocontainers/gtdbtk:2.4.0--pyhdfd78af_1'}"
 
     input:
-    tuple val(meta), path("bins/*")
+    tuple val(meta)   , path("bins/*")
     tuple val(db_name), path("database/*")
-    path(mash_db)
+    path mash_db
 
     output:
-    tuple val(meta), path("gtdbtk.${prefix}.*.summary.tsv")         , emit: summary
-    tuple val(meta), path("gtdbtk.${prefix}.*.classify.tree.gz")    , emit: tree, optional: true
-    tuple val(meta), path("gtdbtk.${prefix}.*.markers_summary.tsv") , emit: markers, optional: true
-    tuple val(meta), path("gtdbtk.${prefix}.*.msa.fasta.gz")        , emit: msa, optional: true
-    tuple val(meta), path("gtdbtk.${prefix}.*.user_msa.fasta.gz")   , emit: user_msa, optional: true
-    tuple val(meta), path("gtdbtk.${prefix}.*.filtered.tsv")        , emit: filtered, optional: true
-    tuple val(meta), path("gtdbtk.${prefix}.failed_genomes.tsv")    , emit: failed, optional: true
-    tuple val(meta), path("gtdbtk.${prefix}.log")                   , emit: log
-    tuple val(meta), path("gtdbtk.${prefix}.warnings.log")          , emit: warnings
-    path("versions.yml")                           , emit: versions
+    tuple val(meta), path("gtdbtk.${prefix}.*.summary.tsv")        , emit: summary
+    tuple val(meta), path("gtdbtk.${prefix}.*.classify.tree.gz")   , emit: tree    , optional: true
+    tuple val(meta), path("gtdbtk.${prefix}.*.markers_summary.tsv"), emit: markers , optional: true
+    tuple val(meta), path("gtdbtk.${prefix}.*.msa.fasta.gz")       , emit: msa     , optional: true
+    tuple val(meta), path("gtdbtk.${prefix}.*.user_msa.fasta.gz")  , emit: user_msa, optional: true
+    tuple val(meta), path("gtdbtk.${prefix}.*.filtered.tsv")       , emit: filtered, optional: true
+    tuple val(meta), path("gtdbtk.${prefix}.failed_genomes.tsv")   , emit: failed  , optional: true
+    tuple val(meta), path("gtdbtk.${prefix}.log")                  , emit: log
+    tuple val(meta), path("gtdbtk.${prefix}.warnings.log")         , emit: warnings
+    path ("versions.yml"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -31,7 +27,7 @@ process GTDBTK_CLASSIFYWF {
     script:
     def args = task.ext.args ?: ''
     def pplacer_scratch = params.gtdbtk_pplacer_scratch ? "--scratch_dir pplacer_tmp" : ""
-    def mash_mode = mash_db ? "--mash_db ${mash_db}" : "--skip_ani_screen"
+    def mash_mode       = mash_db                       ? "--mash_db ${mash_db}"      : "--skip_ani_screen"
     prefix = task.ext.prefix ?: "${meta.id}"
 
     """
@@ -41,27 +37,27 @@ process GTDBTK_CLASSIFYWF {
     fi
 
     gtdbtk classify_wf \\
-        $args \\
+        ${args} \\
         --genome_dir bins \\
         --prefix "gtdbtk.${prefix}" \\
         --out_dir "\${PWD}" \\
-        --cpus $task.cpus \\
-        $mash_mode \\
-        $pplacer_scratch \\
-        --min_perc_aa $params.gtdbtk_min_perc_aa \\
-        --min_af $params.gtdbtk_min_af
+        --cpus ${task.cpus} \\
+        ${mash_mode} \\
+        ${pplacer_scratch} \\
+        --min_perc_aa ${params.gtdbtk_min_perc_aa} \\
+        --min_af ${params.gtdbtk_min_af}
 
     ## If mash db given, classify/ and identify/ directories won't be created
-    if [[ -d classify/ ]]; then
+    if [[ -d classify/ && \$(ls -A classify/) ]]; then
         mv classify/* .
     fi
 
-    if [[ -d identify/ ]]; then
+    if [[ -d identify/ && \$(ls -A identify/) ]]; then
         mv identify/* .
     fi
 
     ## If nothing aligns, no output, so only run
-    if [[ -d align/ ]]; then
+    if [[ -d align/ && \$(ls -A align/) ]]; then
         mv align/* .
     fi
 
@@ -78,7 +74,8 @@ process GTDBTK_CLASSIFYWF {
     """
 
     stub:
-    def VERSION = '2.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def VERSION = '2.3.2'
+    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch gtdbtk.${prefix}.stub.summary.tsv
@@ -93,7 +90,7 @@ process GTDBTK_CLASSIFYWF {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        gtdbtk: \$(echo "$VERSION")
+        gtdbtk: \$(echo "${VERSION}")
     END_VERSIONS
     """
 }

From a60f2e7a9b86dfc31b9bbfcf9154649c19ea6c52 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Mon, 16 Sep 2024 13:07:36 +0200
Subject: [PATCH 11/24] Address comments via ofifical module update

---
 modules.json                                              | 2 +-
 modules/nf-core/gtdbtk/classifywf/main.nf                 | 4 +---
 modules/nf-core/gtdbtk/classifywf/tests/main.nf.test.snap | 8 ++++----
 3 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/modules.json b/modules.json
index 64207e26..be1b1dd3 100644
--- a/modules.json
+++ b/modules.json
@@ -124,7 +124,7 @@
                     },
                     "gtdbtk/classifywf": {
                         "branch": "master",
-                        "git_sha": "c44b5e99aea273adf455d8c40babeb3885083ff9",
+                        "git_sha": "3fb6803fd1cf5a63998216f4254d6d4e487fab21",
                         "installed_by": ["modules"]
                     },
                     "gunc/downloaddb": {
diff --git a/modules/nf-core/gtdbtk/classifywf/main.nf b/modules/nf-core/gtdbtk/classifywf/main.nf
index 9aa13ee4..f0944fdc 100644
--- a/modules/nf-core/gtdbtk/classifywf/main.nf
+++ b/modules/nf-core/gtdbtk/classifywf/main.nf
@@ -74,8 +74,6 @@ process GTDBTK_CLASSIFYWF {
     """
 
     stub:
-    def VERSION = '2.3.2'
-    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch gtdbtk.${prefix}.stub.summary.tsv
@@ -90,7 +88,7 @@ process GTDBTK_CLASSIFYWF {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        gtdbtk: \$(echo "${VERSION}")
+        gtdbtk: \$(echo \$(gtdbtk --version -v 2>&1) | sed "s/gtdbtk: version //; s/ Copyright.*//")
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test.snap b/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test.snap
index e821084c..eb0ee89a 100644
--- a/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test.snap
+++ b/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test.snap
@@ -93,7 +93,7 @@
                     ]
                 ],
                 "9": [
-                    "versions.yml:md5,a8ab755bce9f17684f235d49ab99f6d2"
+                    "versions.yml:md5,2c94de2b8633b99e11881ab0193835d7"
                 ],
                 "failed": [
                     [
@@ -176,7 +176,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,a8ab755bce9f17684f235d49ab99f6d2"
+                    "versions.yml:md5,2c94de2b8633b99e11881ab0193835d7"
                 ],
                 "warnings": [
                     [
@@ -192,8 +192,8 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-26T09:39:21.632259941"
+        "timestamp": "2024-09-16T11:46:32.337929018"
     }
 }
\ No newline at end of file

From b19d4d3d70c33c8acb80c6b2efb8212d378f7a46 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 18 Sep 2024 14:25:37 +0200
Subject: [PATCH 12/24] Utilise missing GTDBK parameters, rename pplacer
 scratch due to suboptimal default

---
 conf/modules.config                           | 188 +++++++++---------
 modules.json                                  |   2 +-
 modules/nf-core/gtdbtk/classifywf/main.nf     |  54 +++--
 modules/nf-core/gtdbtk/classifywf/meta.yml    |   3 +
 .../gtdbtk/classifywf/tests/main.nf.test      |   7 +-
 .../gtdbtk/classifywf/tests/main.nf.test.snap |   8 +-
 nextflow.config                               |   2 +-
 nextflow_schema.json                          |   6 +-
 subworkflows/local/gtdbtk.nf                  |   1 +
 9 files changed, 138 insertions(+), 133 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 81df5bc8..c5afc12b 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -21,18 +21,18 @@ process {
     ]
 
     withName: FASTQC_RAW {
-        ext.args = '--quiet'
+        ext.args   = '--quiet'
         publishDir = [
             path: { "${params.outdir}/QC_shortreads/fastqc" },
             mode: params.publish_dir_mode,
             pattern: "*.html"
         ]
         ext.prefix = { "${meta.id}_run${meta.run}_raw" }
-        tag = { "${meta.id}_run${meta.run}_raw" }
+        tag        = { "${meta.id}_run${meta.run}_raw" }
     }
 
     withName: FASTP {
-        ext.args = [
+        ext.args   = [
             "-q ${params.fastp_qualified_quality}",
             "--cut_front",
             "--cut_tail",
@@ -53,11 +53,11 @@ process {
             ]
         ]
         ext.prefix = { "${meta.id}_run${meta.run}_fastp" }
-        tag = { "${meta.id}_run${meta.run}" }
+        tag        = { "${meta.id}_run${meta.run}" }
     }
 
     withName: ADAPTERREMOVAL_PE {
-        ext.args = [
+        ext.args   = [
             "--minlength ${params.reads_minlength}",
             "--adapter1 ${params.adapterremoval_adapter1} --adapter2 ${params.adapterremoval_adapter2}",
             "--minquality ${params.adapterremoval_minquality} --trimns",
@@ -77,11 +77,11 @@ process {
             ]
         ]
         ext.prefix = { "${meta.id}_run${meta.run}_ar2" }
-        tag = { "${meta.id}_run${meta.run}" }
+        tag        = { "${meta.id}_run${meta.run}" }
     }
 
     withName: ADAPTERREMOVAL_SE {
-        ext.args = [
+        ext.args   = [
             "--minlength ${params.reads_minlength}",
             "--adapter1 ${params.adapterremoval_adapter1}",
             "--minquality ${params.adapterremoval_minquality} --trimns",
@@ -93,7 +93,7 @@ process {
             pattern: "*.{settings}"
         ]
         ext.prefix = { "${meta.id}_run${meta.run}_ar2" }
-        tag = { "${meta.id}_run${meta.run}" }
+        tag        = { "${meta.id}_run${meta.run}" }
     }
 
     withName: BOWTIE2_PHIX_REMOVAL_ALIGN {
@@ -111,12 +111,12 @@ process {
                 enabled: params.save_phixremoved_reads
             ]
         ]
-        tag = { "${meta.id}_run${meta.run}" }
+        tag        = { "${meta.id}_run${meta.run}" }
     }
 
     withName: BOWTIE2_HOST_REMOVAL_ALIGN {
-        ext.args = params.host_removal_verysensitive ? "--very-sensitive" : "--sensitive"
-        ext.args2 = params.host_removal_save_ids ? "--host_removal_save_ids" : ''
+        ext.args   = params.host_removal_verysensitive ? "--very-sensitive" : "--sensitive"
+        ext.args2  = params.host_removal_save_ids ? "--host_removal_save_ids" : ''
         ext.prefix = { "${meta.id}_run${meta.run}_host_removed" }
         publishDir = [
             [
@@ -131,37 +131,37 @@ process {
                 enabled: params.save_hostremoved_reads
             ]
         ]
-        tag = { "${meta.id}_run${meta.run}" }
+        tag        = { "${meta.id}_run${meta.run}" }
     }
 
     withName: FASTQC_TRIMMED {
-        ext.args = '--quiet'
+        ext.args   = '--quiet'
         ext.prefix = { "${meta.id}_run${meta.run}_trimmed" }
         publishDir = [
             path: { "${params.outdir}/QC_shortreads/fastqc" },
             mode: params.publish_dir_mode,
             pattern: "*.html"
         ]
-        tag = { "${meta.id}_run${meta.run}" }
+        tag        = { "${meta.id}_run${meta.run}" }
     }
 
     withName: BBMAP_BBNORM {
-        ext.args = [
+        ext.args   = [
             params.bbnorm_target ? "target=${params.bbnorm_target}" : '',
-            params.bbnorm_min    ? "min=${params.bbnorm_min}"       : '',
+            params.bbnorm_min ? "min=${params.bbnorm_min}" : ''
         ].join(' ').trim()
         publishDir = [
             [
-                path : { "${params.outdir}/bbmap/bbnorm/logs" },
+                path: { "${params.outdir}/bbmap/bbnorm/logs" },
                 enabled: params.save_bbnorm_reads,
-                mode : params.publish_dir_mode,
+                mode: params.publish_dir_mode,
                 pattern: "*.log"
             ],
             [
-                path : { "${params.outdir}/bbmap/bbnorm/"},
-                mode : 'copy',
+                path: { "${params.outdir}/bbmap/bbnorm/" },
+                mode: 'copy',
                 enabled: params.save_bbnorm_reads,
-                mode : params.publish_dir_mode,
+                mode: params.publish_dir_mode,
                 pattern: "*.fastq.gz"
             ]
         ]
@@ -169,21 +169,21 @@ process {
 
     withName: PORECHOP_PORECHOP {
         publishDir = [
-                path: { "${params.outdir}/QC_longreads/porechop" },
-                mode: params.publish_dir_mode,
-                pattern: "*_trimmed.fastq",
-                enabled: params.save_porechop_reads
-            ]
+            path: { "${params.outdir}/QC_longreads/porechop" },
+            mode: params.publish_dir_mode,
+            pattern: "*_trimmed.fastq",
+            enabled: params.save_porechop_reads
+        ]
         ext.prefix = { "${meta.id}_run${meta.run}_trimmed" }
     }
 
     withName: FILTLONG {
         publishDir = [
-                path: { "${params.outdir}/QC_longreads/Filtlong" },
-                mode: params.publish_dir_mode,
-                pattern: "*_lr_filtlong.fastq.gz",
-                enabled: params.save_filtlong_reads
-            ]
+            path: { "${params.outdir}/QC_longreads/Filtlong" },
+            mode: params.publish_dir_mode,
+            pattern: "*_lr_filtlong.fastq.gz",
+            enabled: params.save_filtlong_reads
+        ]
         ext.prefix = { "${meta.id}_run${meta.run}_lengthfiltered" }
     }
 
@@ -206,11 +206,13 @@ process {
 
     withName: NANOPLOT_RAW {
         ext.prefix = 'raw'
-        ext.args = { [
-            "-p raw_",
-            "--title ${meta.id}_raw",
-            "-c darkblue",
-        ].join(' ').trim() }
+        ext.args   = {
+            [
+                "-p raw_",
+                "--title ${meta.id}_raw",
+                "-c darkblue"
+            ].join(' ').trim()
+        }
         publishDir = [
             path: { "${params.outdir}/QC_longreads/NanoPlot/${meta.id}" },
             mode: params.publish_dir_mode,
@@ -219,11 +221,13 @@ process {
     }
 
     withName: NANOPLOT_FILTERED {
-        ext.args = { [
-            "-p filtered_",
-            "--title ${meta.id}_filtered",
-            "-c darkblue",
-        ].join(' ').trim() }
+        ext.args   = {
+            [
+                "-p filtered_",
+                "--title ${meta.id}_filtered",
+                "-c darkblue"
+            ].join(' ').trim()
+        }
         publishDir = [
             path: { "${params.outdir}/QC_longreads/NanoPlot/${meta.id}" },
             mode: params.publish_dir_mode,
@@ -249,7 +253,7 @@ process {
     }
 
     withName: KRAKEN2 {
-        ext.args = '--quiet'
+        ext.args   = '--quiet'
         publishDir = [
             path: { "${params.outdir}/Taxonomy/kraken2/${meta.id}" },
             mode: params.publish_dir_mode,
@@ -276,19 +280,22 @@ process {
 
     //pattern: "*.{fa.gz,log}" //'pattern' didnt work, probably because the output is in a folder, solved with 'saveAs'
     withName: MEGAHIT {
-        ext.args = params.megahit_options ?: ''
+        ext.args   = params.megahit_options ?: ''
         publishDir = [
             path: { "${params.outdir}/Assembly" },
             mode: params.publish_dir_mode,
-            saveAs: {
-                filename -> filename.equals('versions.yml') ? null :
-                filename.indexOf('.contigs.fa.gz') > 0      ? filename :
-                filename.indexOf('.log') > 0                ? filename : null }
+            saveAs: { filename ->
+                filename.equals('versions.yml')
+                    ? null
+                    : filename.indexOf('.contigs.fa.gz') > 0
+                        ? filename
+                        : filename.indexOf('.log') > 0 ? filename : null
+            }
         ]
     }
 
     withName: SPADES {
-        ext.args = params.spades_options ?: ''
+        ext.args   = params.spades_options ?: ''
         publishDir = [
             path: { "${params.outdir}/Assembly/SPAdes" },
             mode: params.publish_dir_mode,
@@ -297,7 +304,7 @@ process {
     }
 
     withName: SPADESHYBRID {
-        ext.args = params.spades_options ?: ''
+        ext.args   = params.spades_options ?: ''
         publishDir = [
             path: { "${params.outdir}/Assembly/SPAdesHybrid" },
             mode: params.publish_dir_mode,
@@ -314,10 +321,10 @@ process {
     }
 
     withName: GENOMAD_ENDTOEND {
-        ext.args = [
+        ext.args   = [
             "--cleanup",
             "--min-score ${params.genomad_min_score}",
-            "--splits ${params.genomad_splits}",
+            "--splits ${params.genomad_splits}"
         ].join(' ').trim()
         publishDir = [
             path: { "${params.outdir}/VirusIdentification/geNomad/${meta.id}" },
@@ -327,7 +334,7 @@ process {
     }
 
     withName: BOWTIE2_ASSEMBLY_ALIGN {
-        ext.args = params.bowtie2_mode ? params.bowtie2_mode : params.ancient_dna ? '--very-sensitive -N 1' : ''
+        ext.args   = params.bowtie2_mode ? params.bowtie2_mode : params.ancient_dna ? '--very-sensitive -N 1' : ''
         ext.prefix = { "${meta.id}.assembly" }
         publishDir = [
             [
@@ -340,7 +347,7 @@ process {
                 mode: params.publish_dir_mode,
                 pattern: "*.{bam,bai}",
                 enabled: params.save_assembly_mapped_reads
-            ],
+            ]
         ]
     }
 
@@ -352,7 +359,7 @@ process {
         ]
     }
 
-    withName: 'BIN_SUMMARY' {
+    withName: BIN_SUMMARY {
         publishDir = [
             path: { "${params.outdir}/GenomeBinning" },
             mode: params.publish_dir_mode,
@@ -368,10 +375,10 @@ process {
         ]
     }
 
-    withName: 'BUSCO' {
-        ext.args = [
-                params.busco_db ? '--offline' : ''
-            ].join(' ').trim()
+    withName: BUSCO {
+        ext.args   = [
+            params.busco_db ? '--offline' : ''
+        ].join(' ').trim()
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC/BUSCO" },
             mode: params.publish_dir_mode,
@@ -406,8 +413,8 @@ process {
         ]
     }
 
-    withName: 'CHECKM_LINEAGEWF' {
-        tag = { "${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}" }
+    withName: CHECKM_LINEAGEWF {
+        tag        = { "${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}" }
         ext.prefix = { "${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}_wf" }
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC/CheckM" },
@@ -416,9 +423,9 @@ process {
         ]
     }
 
-    withName: 'CHECKM_QA' {
+    withName: CHECKM_QA {
         ext.prefix = { "${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}_qa" }
-        ext.args = "-o 2 --tab_table"
+        ext.args   = "-o 2 --tab_table"
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC/CheckM" },
             mode: params.publish_dir_mode,
@@ -426,7 +433,7 @@ process {
         ]
     }
 
-    withName: 'COMBINE_CHECKM_TSV' {
+    withName: COMBINE_CHECKM_TSV {
         ext.prefix = { "checkm_summary" }
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC" },
@@ -435,7 +442,7 @@ process {
         ]
     }
 
-    withName: 'GUNC_DOWNLOADDB' {
+    withName: GUNC_DOWNLOADDB {
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC/GUNC" },
             mode: params.publish_dir_mode,
@@ -445,7 +452,7 @@ process {
     }
 
     // Make sure to keep directory in sync with gunc_qc.nf
-    withName: 'GUNC_RUN' {
+    withName: GUNC_RUN {
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC/GUNC/raw/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}/${fasta.baseName}/" },
             mode: params.publish_dir_mode,
@@ -454,7 +461,7 @@ process {
     }
 
     // Make sure to keep directory in sync with gunc_qc.nf
-    withName: 'GUNC_MERGECHECKM' {
+    withName: GUNC_MERGECHECKM {
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC/GUNC/checkmmerged/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}/${checkm_file.baseName}" },
             mode: params.publish_dir_mode,
@@ -487,7 +494,12 @@ process {
     }
 
     withName: GTDBTK_CLASSIFYWF {
-        ext.args   = "--extension fa"
+        ext.args   = [
+            "--extension fa",
+            "--min_perc_aa ${gtdbtk_min_perc_aa}",
+            "--min_af ${gtdbtk_min_af}",
+            "--pplacer_cpus ${gtdbtk_pplacer_cpus}"
+        ].join(' ')
         ext.prefix = { "${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}" }
         publishDir = [
             path: { "${params.outdir}/Taxonomy/GTDB-Tk/${meta.assembler}/${meta.binner}/${meta.id}" },
@@ -546,7 +558,7 @@ process {
     withName: BCFTOOLS_CONSENSUS {
         ext.prefix = { "${meta.assembler}-${meta.id}" }
         publishDir = [
-            path: {"${params.outdir}/Ancient_DNA/variant_calling/consensus" },
+            path: { "${params.outdir}/Ancient_DNA/variant_calling/consensus" },
             mode: params.publish_dir_mode,
             pattern: "*.fa"
         ]
@@ -556,7 +568,7 @@ process {
         ext.prefix = { "${meta.assembler}-${meta.id}" }
         ext.args   = "-t"
         publishDir = [
-            path: {"${params.outdir}/Ancient_DNA/variant_calling/index" },
+            path: { "${params.outdir}/Ancient_DNA/variant_calling/index" },
             mode: params.publish_dir_mode,
             enabled: false
         ]
@@ -565,7 +577,7 @@ process {
     withName: PYDAMAGE_ANALYZE {
         ext.prefix = { "${meta.assembler}-${meta.id}" }
         publishDir = [
-            path: {"${params.outdir}/Ancient_DNA/pydamage/analyze/${meta.assembler}-${meta.id}/" },
+            path: { "${params.outdir}/Ancient_DNA/pydamage/analyze/${meta.assembler}-${meta.id}/" },
             mode: params.publish_dir_mode
         ]
     }
@@ -574,7 +586,7 @@ process {
         ext.prefix = { "${meta.assembler}-${meta.id}" }
         ext.args   = "-t ${params.pydamage_accuracy}"
         publishDir = [
-            path: {"${params.outdir}/Ancient_DNA/pydamage/filter/${meta.assembler}-${meta.id}/" },
+            path: { "${params.outdir}/Ancient_DNA/pydamage/filter/${meta.assembler}-${meta.id}/" },
             mode: params.publish_dir_mode
         ]
     }
@@ -582,7 +594,7 @@ process {
     withName: SAMTOOLS_FAIDX {
         ext.prefix = { "${meta.assembler}-${meta.id}" }
         publishDir = [
-            path: {"${params.outdir}/Ancient_DNA/samtools/faidx" },
+            path: { "${params.outdir}/Ancient_DNA/samtools/faidx" },
             mode: params.publish_dir_mode,
             enabled: false
         ]
@@ -616,7 +628,7 @@ process {
             ]
         ]
         ext.prefix = { "${meta.assembler}-MetaBAT2-${meta.id}" }
-        ext.args = [
+        ext.args   = [
             params.min_contig_size < 1500 ? "-m 1500" : "-m ${params.min_contig_size}",
             "--unbinned",
             "--seed ${params.metabat_rng_seed}"
@@ -629,11 +641,9 @@ process {
                 path: { "${params.outdir}/GenomeBinning/MaxBin2/discarded" },
                 mode: params.publish_dir_mode,
                 pattern: '*.tooshort.gz'
-            ],
+            ]
         ]
         ext.prefix = { "${meta.assembler}-MaxBin2-${meta.id}" }
-        // if no gene found, will crash so allow ignore so rest of pipeline
-        // completes but without MaxBin2 results
     }
 
     withName: ADJUST_MAXBIN2_EXT {
@@ -642,11 +652,11 @@ process {
                 path: { "${params.outdir}/GenomeBinning/MaxBin2/bins/" },
                 mode: params.publish_dir_mode,
                 pattern: '*.fa.gz'
-            ],
+            ]
         ]
     }
 
-    withName: "CONCOCT_.*" {
+    withName: 'CONCOCT_.*' {
         publishDir = [
             [
                 path: { "${params.outdir}/GenomeBinning/CONCOCT/stats/" },
@@ -705,10 +715,10 @@ process {
                 path: { "${params.outdir}/GenomeBinning/DASTool" },
                 mode: params.publish_dir_mode,
                 pattern: '*.{tsv,log,eval,seqlength}'
-            ],
+            ]
         ]
         ext.prefix = { "${meta.assembler}-DASTool-${meta.id}" }
-        ext.args = "--write_bins --write_unbinned --write_bin_evals --score_threshold ${params.refine_bins_dastool_threshold}"
+        ext.args   = "--write_bins --write_unbinned --write_bin_evals --score_threshold ${params.refine_bins_dastool_threshold}"
     }
 
     withName: RENAME_POSTDASTOOL {
@@ -721,7 +731,6 @@ process {
             [
                 path: { "${params.outdir}/GenomeBinning/DASTool/bins" },
                 mode: params.publish_dir_mode,
-                // pattern needs to be updated in case of new binning methods
                 pattern: '*-{MetaBAT2,MaxBin2,CONCOCT}Refined-*.fa'
             ]
         ]
@@ -729,16 +738,16 @@ process {
 
     withName: TIARA_TIARA {
         publishDir = [
-                path: { "${params.outdir}/Taxonomy/Tiara/" },
-                mode: params.publish_dir_mode,
-                pattern: "*.txt"
-            ]
-        ext.args = { "--min_len ${params.tiara_min_length} --probabilities" }
+            path: { "${params.outdir}/Taxonomy/Tiara/" },
+            mode: params.publish_dir_mode,
+            pattern: "*.txt"
+        ]
+        ext.args   = { "--min_len ${params.tiara_min_length} --probabilities" }
         ext.prefix = { "${meta.assembler}-${meta.id}.tiara" }
     }
 
     withName: TIARA_CLASSIFY {
-        ext.args = { "--join_prokaryotes --assembler ${meta.assembler}" }
+        ext.args   = { "--join_prokaryotes --assembler ${meta.assembler}" }
         ext.prefix = { "${meta.assembler}-${meta.binner}-${meta.bin}-${meta.id}" }
     }
 
@@ -771,13 +780,12 @@ process {
         ]
     }
 
-    withName: 'MULTIQC' {
-        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+    withName: MULTIQC {
+        ext.args   = { params.multiqc_title ? "--title \"${params.multiqc_title}\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-
 }
diff --git a/modules.json b/modules.json
index b17f7dc3..5f4eb8bb 100644
--- a/modules.json
+++ b/modules.json
@@ -124,7 +124,7 @@
                     },
                     "gtdbtk/classifywf": {
                         "branch": "master",
-                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+                        "git_sha": "7b9ce4b817926f17ec82cc0099d2d0ff095a2fac",
                         "installed_by": ["modules"]
                     },
                     "gunc/downloaddb": {
diff --git a/modules/nf-core/gtdbtk/classifywf/main.nf b/modules/nf-core/gtdbtk/classifywf/main.nf
index 9fc7a32d..23862fee 100644
--- a/modules/nf-core/gtdbtk/classifywf/main.nf
+++ b/modules/nf-core/gtdbtk/classifywf/main.nf
@@ -1,37 +1,34 @@
 process GTDBTK_CLASSIFYWF {
     tag "${prefix}"
     label 'process_medium'
-
-    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gtdbtk:2.4.0--pyhdfd78af_1' :
-        'biocontainers/gtdbtk:2.4.0--pyhdfd78af_1' }"
+    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gtdbtk:2.4.0--pyhdfd78af_1' : 'biocontainers/gtdbtk:2.4.0--pyhdfd78af_1'}"
 
     input:
-    tuple val(meta), path("bins/*")
+    tuple val(meta)   , path("bins/*")
     tuple val(db_name), path("database/*")
-    path(mash_db)
+    val use_pplacer_scratch_dir
+    path mash_db
 
     output:
-    tuple val(meta), path("gtdbtk.${prefix}.*.summary.tsv")         , emit: summary
-    tuple val(meta), path("gtdbtk.${prefix}.*.classify.tree.gz")    , emit: tree, optional: true
-    tuple val(meta), path("gtdbtk.${prefix}.*.markers_summary.tsv") , emit: markers, optional: true
-    tuple val(meta), path("gtdbtk.${prefix}.*.msa.fasta.gz")        , emit: msa, optional: true
-    tuple val(meta), path("gtdbtk.${prefix}.*.user_msa.fasta.gz")   , emit: user_msa, optional: true
-    tuple val(meta), path("gtdbtk.${prefix}.*.filtered.tsv")        , emit: filtered, optional: true
-    tuple val(meta), path("gtdbtk.${prefix}.failed_genomes.tsv")    , emit: failed, optional: true
-    tuple val(meta), path("gtdbtk.${prefix}.log")                   , emit: log
-    tuple val(meta), path("gtdbtk.${prefix}.warnings.log")          , emit: warnings
-    path("versions.yml")                           , emit: versions
+    tuple val(meta), path("gtdbtk.${prefix}.*.summary.tsv")        , emit: summary
+    tuple val(meta), path("gtdbtk.${prefix}.*.classify.tree.gz")   , emit: tree    , optional: true
+    tuple val(meta), path("gtdbtk.${prefix}.*.markers_summary.tsv"), emit: markers , optional: true
+    tuple val(meta), path("gtdbtk.${prefix}.*.msa.fasta.gz")       , emit: msa     , optional: true
+    tuple val(meta), path("gtdbtk.${prefix}.*.user_msa.fasta.gz")  , emit: user_msa, optional: true
+    tuple val(meta), path("gtdbtk.${prefix}.*.filtered.tsv")       , emit: filtered, optional: true
+    tuple val(meta), path("gtdbtk.${prefix}.failed_genomes.tsv")   , emit: failed  , optional: true
+    tuple val(meta), path("gtdbtk.${prefix}.log")                  , emit: log
+    tuple val(meta), path("gtdbtk.${prefix}.warnings.log")         , emit: warnings
+    path ("versions.yml"), emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def pplacer_scratch = params.gtdbtk_pplacer_scratch ? "--scratch_dir pplacer_tmp" : ""
-    def mash_mode = mash_db ? "--mash_db ${mash_db}" : "--skip_ani_screen"
+    def pplacer_scratch = use_pplacer_scratch_dir ? "--scratch_dir pplacer_tmp" : ""
+    def mash_mode       = mash_db                 ? "--mash_db ${mash_db}"      : "--skip_ani_screen"
     prefix = task.ext.prefix ?: "${meta.id}"
 
     """
@@ -41,27 +38,25 @@ process GTDBTK_CLASSIFYWF {
     fi
 
     gtdbtk classify_wf \\
-        $args \\
+        ${args} \\
         --genome_dir bins \\
         --prefix "gtdbtk.${prefix}" \\
         --out_dir "\${PWD}" \\
-        --cpus $task.cpus \\
-        $mash_mode \\
-        $pplacer_scratch \\
-        --min_perc_aa $params.gtdbtk_min_perc_aa \\
-        --min_af $params.gtdbtk_min_af
+        --cpus ${task.cpus} \\
+        ${mash_mode} \\
+        ${pplacer_scratch}
 
     ## If mash db given, classify/ and identify/ directories won't be created
-    if [[ -d classify/ ]]; then
+    if [[ -d classify/ && \$(ls -A classify/) ]]; then
         mv classify/* .
     fi
 
-    if [[ -d identify/ ]]; then
+    if [[ -d identify/ && \$(ls -A identify/) ]]; then
         mv identify/* .
     fi
 
     ## If nothing aligns, no output, so only run
-    if [[ -d align/ ]]; then
+    if [[ -d align/ && \$(ls -A align/) ]]; then
         mv align/* .
     fi
 
@@ -78,7 +73,6 @@ process GTDBTK_CLASSIFYWF {
     """
 
     stub:
-    def VERSION = '2.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch gtdbtk.${prefix}.stub.summary.tsv
@@ -93,7 +87,7 @@ process GTDBTK_CLASSIFYWF {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        gtdbtk: \$(echo "$VERSION")
+        gtdbtk: \$(echo \$(gtdbtk --version -v 2>&1) | sed "s/gtdbtk: version //; s/ Copyright.*//")
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/gtdbtk/classifywf/meta.yml b/modules/nf-core/gtdbtk/classifywf/meta.yml
index d85f9966..0667dcd6 100644
--- a/modules/nf-core/gtdbtk/classifywf/meta.yml
+++ b/modules/nf-core/gtdbtk/classifywf/meta.yml
@@ -30,6 +30,9 @@ input:
       type: file
       description: The local copy of the taxonomic database used by GTDB-tk (unzipped copy)
       pattern: "*"
+  - use_pplacer_scratch_dir:
+      type: boolean
+      description: Set to true to reduce pplacer memory usage by writing to disk (slower)
   - mash_db:
       type: file
       description: The local copy of the Mash sketch database used by GTDB-tk if `ani_screen` mode is used (optional)
diff --git a/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test b/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test
index 60bedb68..deca962d 100644
--- a/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test
+++ b/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test
@@ -26,7 +26,8 @@ nextflow_process {
                         ]
                     ]
                 input[1] = [[], []]
-                input[2] = []
+                input[2] = false
+                input[3] = []
                 """
             }
         }
@@ -35,9 +36,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out).match() }
-           )
+            )
         }
-
     }
-
 }
diff --git a/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test.snap b/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test.snap
index e821084c..eb0ee89a 100644
--- a/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test.snap
+++ b/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test.snap
@@ -93,7 +93,7 @@
                     ]
                 ],
                 "9": [
-                    "versions.yml:md5,a8ab755bce9f17684f235d49ab99f6d2"
+                    "versions.yml:md5,2c94de2b8633b99e11881ab0193835d7"
                 ],
                 "failed": [
                     [
@@ -176,7 +176,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,a8ab755bce9f17684f235d49ab99f6d2"
+                    "versions.yml:md5,2c94de2b8633b99e11881ab0193835d7"
                 ],
                 "warnings": [
                     [
@@ -192,8 +192,8 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-03-26T09:39:21.632259941"
+        "timestamp": "2024-09-16T11:46:32.337929018"
     }
 }
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index faab3eba..849922d9 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -95,7 +95,7 @@ params {
     gtdbtk_min_perc_aa                   = 10
     gtdbtk_min_af                        = 0.65
     gtdbtk_pplacer_cpus                  = 1
-    gtdbtk_pplacer_scratch               = true
+    gtdbtk_pplacer_scratchoff            = false
 
     // long read preprocessing options
     skip_adapter_trimming                = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 6b6b4c07..78ccdabc 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -584,11 +584,11 @@
                     "description": "Number of CPUs used for the by GTDB-Tk run tool pplacer.",
                     "help_text": "A low number of CPUs helps to reduce the memory required/reported by GTDB-Tk. See also the [GTDB-Tk documentation](https://ecogenomics.github.io/GTDBTk/faq.html#gtdb-tk-reaches-the-memory-limit-pplacer-crashes)."
                 },
-                "gtdbtk_pplacer_scratch": {
+                "gtdbtk_pplacer_scratchoff": {
                     "type": "boolean",
                     "default": true,
-                    "description": "Reduce GTDB-Tk memory consumption by running pplacer in a setting writing to disk.",
-                    "help_text": "Will be slower. Set to `false` to turn this off."
+                    "description": "Speed up pplacer step of GTDB-Tk by loading to memory.",
+                    "help_text": "Will be faster than writing to disk (default setting), however at the expense of much larger memory (RAM) requirements for GDTBTK/CLASSIFY."
                 },
                 "genomad_db": {
                     "type": "string",
diff --git a/subworkflows/local/gtdbtk.nf b/subworkflows/local/gtdbtk.nf
index 21ef25b2..c5893f16 100644
--- a/subworkflows/local/gtdbtk.nf
+++ b/subworkflows/local/gtdbtk.nf
@@ -90,6 +90,7 @@ workflow GTDBTK {
     GTDBTK_CLASSIFYWF (
         ch_filtered_bins.passed.groupTuple(),
         ch_db_for_gtdbtk,
+        params.gtdbtk_pplacer_scratchoff ? false : true
         gtdb_mash
     )
 

From 1059e3658649757b05a37856df7b18e7fba0074e Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 18 Sep 2024 14:29:17 +0200
Subject: [PATCH 13/24] Update CHANGELOG

---
 CHANGELOG.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 08c3c625..0a310d99 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#665](https://github.com/nf-core/mag/pull/648) - Add support for supplying pre-made bowtie host reference index (requested by @simone-pignotti, added by @jfy133)
+- [#670](https://github.com/nf-core/mag/pull/670) - Added --gtdbtk_pplacer_scratchoff to run GTDBTk in memory mode rather than write to disk (reported by harper357, fixed by @jfy133)
 
 ### `Changed`
 
@@ -16,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 
 - [#667](https://github.com/nf-core/mag/pull/667) - Fix pipeline crashing if only CONCOCT selected during binning (reported and fixed by @jfy133)
+- [#670](https://github.com/nf-core/mag/pull/670) - Re-add missing GTDBTk parameters into GTDBTk module (reported by harper357, fixed by @jfy133)
 
 ### `Dependencies`
 
@@ -25,6 +27,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
+- [#670](https://github.com/nf-core/mag/pull/670) - Deprecated --gtdbtk_pplacer_scratch due to uninuitive usage (reported by harper357, fixed by @jfy133)
+
 ## 3.0.3 [2024-08-27]
 
 ### `Added`

From a3ce46a3ccfd620cf9eda8ae52fe425a148e660d Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 18 Sep 2024 14:35:31 +0200
Subject: [PATCH 14/24] Specify they are parameters

---
 conf/modules.config | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index c5afc12b..44d8fbbc 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -496,9 +496,9 @@ process {
     withName: GTDBTK_CLASSIFYWF {
         ext.args   = [
             "--extension fa",
-            "--min_perc_aa ${gtdbtk_min_perc_aa}",
-            "--min_af ${gtdbtk_min_af}",
-            "--pplacer_cpus ${gtdbtk_pplacer_cpus}"
+            "--min_perc_aa ${params.gtdbtk_min_perc_aa}",
+            "--min_af ${params.gtdbtk_min_af}",
+            "--pplacer_cpus ${params.gtdbtk_pplacer_cpus}"
         ].join(' ')
         ext.prefix = { "${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}" }
         publishDir = [

From 459f41853d4fe7e18d9c3eb9500e557e55f79f1d Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Fri, 20 Sep 2024 14:27:04 +0200
Subject: [PATCH 15/24] Typo fixes after review from @harper357

---
 CHANGELOG.md                 | 2 +-
 subworkflows/local/gtdbtk.nf | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0a310d99..abd2b0c0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#665](https://github.com/nf-core/mag/pull/648) - Add support for supplying pre-made bowtie host reference index (requested by @simone-pignotti, added by @jfy133)
-- [#670](https://github.com/nf-core/mag/pull/670) - Added --gtdbtk_pplacer_scratchoff to run GTDBTk in memory mode rather than write to disk (reported by harper357, fixed by @jfy133)
+- [#670](https://github.com/nf-core/mag/pull/670) - Added --gtdbtk_pplacer_scratchoff to run GTDBTk in memory mode rather than write to disk (reported by @harper357, fixed by @jfy133)
 
 ### `Changed`
 
diff --git a/subworkflows/local/gtdbtk.nf b/subworkflows/local/gtdbtk.nf
index c5893f16..0216e27a 100644
--- a/subworkflows/local/gtdbtk.nf
+++ b/subworkflows/local/gtdbtk.nf
@@ -90,7 +90,7 @@ workflow GTDBTK {
     GTDBTK_CLASSIFYWF (
         ch_filtered_bins.passed.groupTuple(),
         ch_db_for_gtdbtk,
-        params.gtdbtk_pplacer_scratchoff ? false : true
+        params.gtdbtk_pplacer_scratchoff ? false : true,
         gtdb_mash
     )
 

From 6183ef013d4a2072da24afe153a3fa7b0c9dce3b Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Fri, 20 Sep 2024 14:33:37 +0200
Subject: [PATCH 16/24] REname scratchoff to more intiuitive name to match
 behaviour

---
 CHANGELOG.md                 | 4 ++--
 nextflow.config              | 2 +-
 nextflow_schema.json         | 4 ++--
 subworkflows/local/gtdbtk.nf | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index abd2b0c0..99765627 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Added`
 
 - [#665](https://github.com/nf-core/mag/pull/648) - Add support for supplying pre-made bowtie host reference index (requested by @simone-pignotti, added by @jfy133)
-- [#670](https://github.com/nf-core/mag/pull/670) - Added --gtdbtk_pplacer_scratchoff to run GTDBTk in memory mode rather than write to disk (reported by @harper357, fixed by @jfy133)
+- [#670](https://github.com/nf-core/mag/pull/670) - Added --gtdbtk_pplacer_useram to run GTDBTk in memory mode rather than write to disk (reported by @harper357, fixed by @jfy133)
 
 ### `Changed`
 
@@ -27,7 +27,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
-- [#670](https://github.com/nf-core/mag/pull/670) - Deprecated --gtdbtk_pplacer_scratch due to uninuitive usage (reported by harper357, fixed by @jfy133)
+- [#670](https://github.com/nf-core/mag/pull/670) - Deprecated --gtdbtk_pplacer_scratch due to unintuitive usage (reported by harper357, fixed by @jfy133)
 
 ## 3.0.3 [2024-08-27]
 
diff --git a/nextflow.config b/nextflow.config
index 849922d9..3b43df33 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -95,7 +95,7 @@ params {
     gtdbtk_min_perc_aa                   = 10
     gtdbtk_min_af                        = 0.65
     gtdbtk_pplacer_cpus                  = 1
-    gtdbtk_pplacer_scratchoff            = false
+    gtdbtk_pplacer_useram            = false
 
     // long read preprocessing options
     skip_adapter_trimming                = false
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 78ccdabc..dab2eb50 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -584,9 +584,9 @@
                     "description": "Number of CPUs used for the by GTDB-Tk run tool pplacer.",
                     "help_text": "A low number of CPUs helps to reduce the memory required/reported by GTDB-Tk. See also the [GTDB-Tk documentation](https://ecogenomics.github.io/GTDBTk/faq.html#gtdb-tk-reaches-the-memory-limit-pplacer-crashes)."
                 },
-                "gtdbtk_pplacer_scratchoff": {
+                "gtdbtk_pplacer_useram": {
                     "type": "boolean",
-                    "default": true,
+                    "default": false,
                     "description": "Speed up pplacer step of GTDB-Tk by loading to memory.",
                     "help_text": "Will be faster than writing to disk (default setting), however at the expense of much larger memory (RAM) requirements for GDTBTK/CLASSIFY."
                 },
diff --git a/subworkflows/local/gtdbtk.nf b/subworkflows/local/gtdbtk.nf
index 0216e27a..6da5680d 100644
--- a/subworkflows/local/gtdbtk.nf
+++ b/subworkflows/local/gtdbtk.nf
@@ -90,7 +90,7 @@ workflow GTDBTK {
     GTDBTK_CLASSIFYWF (
         ch_filtered_bins.passed.groupTuple(),
         ch_db_for_gtdbtk,
-        params.gtdbtk_pplacer_scratchoff ? false : true,
+        params.gtdbtk_pplacer_useram ? false : true,
         gtdb_mash
     )
 

From 3b199432cd4e5332138dcfa7d7c40351ca1e1486 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Fri, 20 Sep 2024 14:48:20 +0200
Subject: [PATCH 17/24] Fix missing GTDBTk files in outdir

---
 CHANGELOG.md        |   1 +
 conf/modules.config | 183 ++++++++++++++++++++++----------------------
 2 files changed, 94 insertions(+), 90 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 08c3c625..31ae78bd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 
 - [#667](https://github.com/nf-core/mag/pull/667) - Fix pipeline crashing if only CONCOCT selected during binning (reported and fixed by @jfy133)
+- [#672](https://github.com/nf-core/mag/pull/672) - Fix GTDB-Tk per-sample TSV files not being published in output directory (reported by @jhayer, fix by @jfy133)
 
 ### `Dependencies`
 
diff --git a/conf/modules.config b/conf/modules.config
index 81df5bc8..b786a072 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -21,18 +21,18 @@ process {
     ]
 
     withName: FASTQC_RAW {
-        ext.args = '--quiet'
+        ext.args   = '--quiet'
         publishDir = [
             path: { "${params.outdir}/QC_shortreads/fastqc" },
             mode: params.publish_dir_mode,
             pattern: "*.html"
         ]
         ext.prefix = { "${meta.id}_run${meta.run}_raw" }
-        tag = { "${meta.id}_run${meta.run}_raw" }
+        tag        = { "${meta.id}_run${meta.run}_raw" }
     }
 
     withName: FASTP {
-        ext.args = [
+        ext.args   = [
             "-q ${params.fastp_qualified_quality}",
             "--cut_front",
             "--cut_tail",
@@ -53,11 +53,11 @@ process {
             ]
         ]
         ext.prefix = { "${meta.id}_run${meta.run}_fastp" }
-        tag = { "${meta.id}_run${meta.run}" }
+        tag        = { "${meta.id}_run${meta.run}" }
     }
 
     withName: ADAPTERREMOVAL_PE {
-        ext.args = [
+        ext.args   = [
             "--minlength ${params.reads_minlength}",
             "--adapter1 ${params.adapterremoval_adapter1} --adapter2 ${params.adapterremoval_adapter2}",
             "--minquality ${params.adapterremoval_minquality} --trimns",
@@ -77,11 +77,11 @@ process {
             ]
         ]
         ext.prefix = { "${meta.id}_run${meta.run}_ar2" }
-        tag = { "${meta.id}_run${meta.run}" }
+        tag        = { "${meta.id}_run${meta.run}" }
     }
 
     withName: ADAPTERREMOVAL_SE {
-        ext.args = [
+        ext.args   = [
             "--minlength ${params.reads_minlength}",
             "--adapter1 ${params.adapterremoval_adapter1}",
             "--minquality ${params.adapterremoval_minquality} --trimns",
@@ -93,7 +93,7 @@ process {
             pattern: "*.{settings}"
         ]
         ext.prefix = { "${meta.id}_run${meta.run}_ar2" }
-        tag = { "${meta.id}_run${meta.run}" }
+        tag        = { "${meta.id}_run${meta.run}" }
     }
 
     withName: BOWTIE2_PHIX_REMOVAL_ALIGN {
@@ -111,12 +111,12 @@ process {
                 enabled: params.save_phixremoved_reads
             ]
         ]
-        tag = { "${meta.id}_run${meta.run}" }
+        tag        = { "${meta.id}_run${meta.run}" }
     }
 
     withName: BOWTIE2_HOST_REMOVAL_ALIGN {
-        ext.args = params.host_removal_verysensitive ? "--very-sensitive" : "--sensitive"
-        ext.args2 = params.host_removal_save_ids ? "--host_removal_save_ids" : ''
+        ext.args   = params.host_removal_verysensitive ? "--very-sensitive" : "--sensitive"
+        ext.args2  = params.host_removal_save_ids ? "--host_removal_save_ids" : ''
         ext.prefix = { "${meta.id}_run${meta.run}_host_removed" }
         publishDir = [
             [
@@ -131,37 +131,37 @@ process {
                 enabled: params.save_hostremoved_reads
             ]
         ]
-        tag = { "${meta.id}_run${meta.run}" }
+        tag        = { "${meta.id}_run${meta.run}" }
     }
 
     withName: FASTQC_TRIMMED {
-        ext.args = '--quiet'
+        ext.args   = '--quiet'
         ext.prefix = { "${meta.id}_run${meta.run}_trimmed" }
         publishDir = [
             path: { "${params.outdir}/QC_shortreads/fastqc" },
             mode: params.publish_dir_mode,
             pattern: "*.html"
         ]
-        tag = { "${meta.id}_run${meta.run}" }
+        tag        = { "${meta.id}_run${meta.run}" }
     }
 
     withName: BBMAP_BBNORM {
-        ext.args = [
+        ext.args   = [
             params.bbnorm_target ? "target=${params.bbnorm_target}" : '',
-            params.bbnorm_min    ? "min=${params.bbnorm_min}"       : '',
+            params.bbnorm_min ? "min=${params.bbnorm_min}" : ''
         ].join(' ').trim()
         publishDir = [
             [
-                path : { "${params.outdir}/bbmap/bbnorm/logs" },
+                path: { "${params.outdir}/bbmap/bbnorm/logs" },
                 enabled: params.save_bbnorm_reads,
-                mode : params.publish_dir_mode,
+                mode: params.publish_dir_mode,
                 pattern: "*.log"
             ],
             [
-                path : { "${params.outdir}/bbmap/bbnorm/"},
-                mode : 'copy',
+                path: { "${params.outdir}/bbmap/bbnorm/" },
+                mode: 'copy',
                 enabled: params.save_bbnorm_reads,
-                mode : params.publish_dir_mode,
+                mode: params.publish_dir_mode,
                 pattern: "*.fastq.gz"
             ]
         ]
@@ -169,21 +169,21 @@ process {
 
     withName: PORECHOP_PORECHOP {
         publishDir = [
-                path: { "${params.outdir}/QC_longreads/porechop" },
-                mode: params.publish_dir_mode,
-                pattern: "*_trimmed.fastq",
-                enabled: params.save_porechop_reads
-            ]
+            path: { "${params.outdir}/QC_longreads/porechop" },
+            mode: params.publish_dir_mode,
+            pattern: "*_trimmed.fastq",
+            enabled: params.save_porechop_reads
+        ]
         ext.prefix = { "${meta.id}_run${meta.run}_trimmed" }
     }
 
     withName: FILTLONG {
         publishDir = [
-                path: { "${params.outdir}/QC_longreads/Filtlong" },
-                mode: params.publish_dir_mode,
-                pattern: "*_lr_filtlong.fastq.gz",
-                enabled: params.save_filtlong_reads
-            ]
+            path: { "${params.outdir}/QC_longreads/Filtlong" },
+            mode: params.publish_dir_mode,
+            pattern: "*_lr_filtlong.fastq.gz",
+            enabled: params.save_filtlong_reads
+        ]
         ext.prefix = { "${meta.id}_run${meta.run}_lengthfiltered" }
     }
 
@@ -206,11 +206,13 @@ process {
 
     withName: NANOPLOT_RAW {
         ext.prefix = 'raw'
-        ext.args = { [
-            "-p raw_",
-            "--title ${meta.id}_raw",
-            "-c darkblue",
-        ].join(' ').trim() }
+        ext.args   = {
+            [
+                "-p raw_",
+                "--title ${meta.id}_raw",
+                "-c darkblue"
+            ].join(' ').trim()
+        }
         publishDir = [
             path: { "${params.outdir}/QC_longreads/NanoPlot/${meta.id}" },
             mode: params.publish_dir_mode,
@@ -219,11 +221,13 @@ process {
     }
 
     withName: NANOPLOT_FILTERED {
-        ext.args = { [
-            "-p filtered_",
-            "--title ${meta.id}_filtered",
-            "-c darkblue",
-        ].join(' ').trim() }
+        ext.args   = {
+            [
+                "-p filtered_",
+                "--title ${meta.id}_filtered",
+                "-c darkblue"
+            ].join(' ').trim()
+        }
         publishDir = [
             path: { "${params.outdir}/QC_longreads/NanoPlot/${meta.id}" },
             mode: params.publish_dir_mode,
@@ -249,7 +253,7 @@ process {
     }
 
     withName: KRAKEN2 {
-        ext.args = '--quiet'
+        ext.args   = '--quiet'
         publishDir = [
             path: { "${params.outdir}/Taxonomy/kraken2/${meta.id}" },
             mode: params.publish_dir_mode,
@@ -276,19 +280,22 @@ process {
 
     //pattern: "*.{fa.gz,log}" //'pattern' didnt work, probably because the output is in a folder, solved with 'saveAs'
     withName: MEGAHIT {
-        ext.args = params.megahit_options ?: ''
+        ext.args   = params.megahit_options ?: ''
         publishDir = [
             path: { "${params.outdir}/Assembly" },
             mode: params.publish_dir_mode,
-            saveAs: {
-                filename -> filename.equals('versions.yml') ? null :
-                filename.indexOf('.contigs.fa.gz') > 0      ? filename :
-                filename.indexOf('.log') > 0                ? filename : null }
+            saveAs: { filename ->
+                filename.equals('versions.yml')
+                    ? null
+                    : filename.indexOf('.contigs.fa.gz') > 0
+                        ? filename
+                        : filename.indexOf('.log') > 0 ? filename : null
+            }
         ]
     }
 
     withName: SPADES {
-        ext.args = params.spades_options ?: ''
+        ext.args   = params.spades_options ?: ''
         publishDir = [
             path: { "${params.outdir}/Assembly/SPAdes" },
             mode: params.publish_dir_mode,
@@ -297,7 +304,7 @@ process {
     }
 
     withName: SPADESHYBRID {
-        ext.args = params.spades_options ?: ''
+        ext.args   = params.spades_options ?: ''
         publishDir = [
             path: { "${params.outdir}/Assembly/SPAdesHybrid" },
             mode: params.publish_dir_mode,
@@ -314,10 +321,10 @@ process {
     }
 
     withName: GENOMAD_ENDTOEND {
-        ext.args = [
+        ext.args   = [
             "--cleanup",
             "--min-score ${params.genomad_min_score}",
-            "--splits ${params.genomad_splits}",
+            "--splits ${params.genomad_splits}"
         ].join(' ').trim()
         publishDir = [
             path: { "${params.outdir}/VirusIdentification/geNomad/${meta.id}" },
@@ -327,7 +334,7 @@ process {
     }
 
     withName: BOWTIE2_ASSEMBLY_ALIGN {
-        ext.args = params.bowtie2_mode ? params.bowtie2_mode : params.ancient_dna ? '--very-sensitive -N 1' : ''
+        ext.args   = params.bowtie2_mode ? params.bowtie2_mode : params.ancient_dna ? '--very-sensitive -N 1' : ''
         ext.prefix = { "${meta.id}.assembly" }
         publishDir = [
             [
@@ -340,7 +347,7 @@ process {
                 mode: params.publish_dir_mode,
                 pattern: "*.{bam,bai}",
                 enabled: params.save_assembly_mapped_reads
-            ],
+            ]
         ]
     }
 
@@ -352,7 +359,7 @@ process {
         ]
     }
 
-    withName: 'BIN_SUMMARY' {
+    withName: BIN_SUMMARY {
         publishDir = [
             path: { "${params.outdir}/GenomeBinning" },
             mode: params.publish_dir_mode,
@@ -368,10 +375,10 @@ process {
         ]
     }
 
-    withName: 'BUSCO' {
-        ext.args = [
-                params.busco_db ? '--offline' : ''
-            ].join(' ').trim()
+    withName: BUSCO {
+        ext.args   = [
+            params.busco_db ? '--offline' : ''
+        ].join(' ').trim()
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC/BUSCO" },
             mode: params.publish_dir_mode,
@@ -406,8 +413,8 @@ process {
         ]
     }
 
-    withName: 'CHECKM_LINEAGEWF' {
-        tag = { "${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}" }
+    withName: CHECKM_LINEAGEWF {
+        tag        = { "${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}" }
         ext.prefix = { "${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}_wf" }
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC/CheckM" },
@@ -416,9 +423,9 @@ process {
         ]
     }
 
-    withName: 'CHECKM_QA' {
+    withName: CHECKM_QA {
         ext.prefix = { "${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}_qa" }
-        ext.args = "-o 2 --tab_table"
+        ext.args   = "-o 2 --tab_table"
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC/CheckM" },
             mode: params.publish_dir_mode,
@@ -426,7 +433,7 @@ process {
         ]
     }
 
-    withName: 'COMBINE_CHECKM_TSV' {
+    withName: COMBINE_CHECKM_TSV {
         ext.prefix = { "checkm_summary" }
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC" },
@@ -435,7 +442,7 @@ process {
         ]
     }
 
-    withName: 'GUNC_DOWNLOADDB' {
+    withName: GUNC_DOWNLOADDB {
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC/GUNC" },
             mode: params.publish_dir_mode,
@@ -445,7 +452,7 @@ process {
     }
 
     // Make sure to keep directory in sync with gunc_qc.nf
-    withName: 'GUNC_RUN' {
+    withName: GUNC_RUN {
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC/GUNC/raw/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}/${fasta.baseName}/" },
             mode: params.publish_dir_mode,
@@ -454,7 +461,7 @@ process {
     }
 
     // Make sure to keep directory in sync with gunc_qc.nf
-    withName: 'GUNC_MERGECHECKM' {
+    withName: GUNC_MERGECHECKM {
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC/GUNC/checkmmerged/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}/${checkm_file.baseName}" },
             mode: params.publish_dir_mode,
@@ -492,7 +499,7 @@ process {
         publishDir = [
             path: { "${params.outdir}/Taxonomy/GTDB-Tk/${meta.assembler}/${meta.binner}/${meta.id}" },
             mode: params.publish_dir_mode,
-            pattern: "*.{log,tasv,tree.gz,fasta,fasta.gz}"
+            pattern: "*.{log,tsv,tree.gz,fasta,fasta.gz}"
         ]
     }
 
@@ -546,7 +553,7 @@ process {
     withName: BCFTOOLS_CONSENSUS {
         ext.prefix = { "${meta.assembler}-${meta.id}" }
         publishDir = [
-            path: {"${params.outdir}/Ancient_DNA/variant_calling/consensus" },
+            path: { "${params.outdir}/Ancient_DNA/variant_calling/consensus" },
             mode: params.publish_dir_mode,
             pattern: "*.fa"
         ]
@@ -556,7 +563,7 @@ process {
         ext.prefix = { "${meta.assembler}-${meta.id}" }
         ext.args   = "-t"
         publishDir = [
-            path: {"${params.outdir}/Ancient_DNA/variant_calling/index" },
+            path: { "${params.outdir}/Ancient_DNA/variant_calling/index" },
             mode: params.publish_dir_mode,
             enabled: false
         ]
@@ -565,7 +572,7 @@ process {
     withName: PYDAMAGE_ANALYZE {
         ext.prefix = { "${meta.assembler}-${meta.id}" }
         publishDir = [
-            path: {"${params.outdir}/Ancient_DNA/pydamage/analyze/${meta.assembler}-${meta.id}/" },
+            path: { "${params.outdir}/Ancient_DNA/pydamage/analyze/${meta.assembler}-${meta.id}/" },
             mode: params.publish_dir_mode
         ]
     }
@@ -574,7 +581,7 @@ process {
         ext.prefix = { "${meta.assembler}-${meta.id}" }
         ext.args   = "-t ${params.pydamage_accuracy}"
         publishDir = [
-            path: {"${params.outdir}/Ancient_DNA/pydamage/filter/${meta.assembler}-${meta.id}/" },
+            path: { "${params.outdir}/Ancient_DNA/pydamage/filter/${meta.assembler}-${meta.id}/" },
             mode: params.publish_dir_mode
         ]
     }
@@ -582,7 +589,7 @@ process {
     withName: SAMTOOLS_FAIDX {
         ext.prefix = { "${meta.assembler}-${meta.id}" }
         publishDir = [
-            path: {"${params.outdir}/Ancient_DNA/samtools/faidx" },
+            path: { "${params.outdir}/Ancient_DNA/samtools/faidx" },
             mode: params.publish_dir_mode,
             enabled: false
         ]
@@ -616,7 +623,7 @@ process {
             ]
         ]
         ext.prefix = { "${meta.assembler}-MetaBAT2-${meta.id}" }
-        ext.args = [
+        ext.args   = [
             params.min_contig_size < 1500 ? "-m 1500" : "-m ${params.min_contig_size}",
             "--unbinned",
             "--seed ${params.metabat_rng_seed}"
@@ -629,11 +636,9 @@ process {
                 path: { "${params.outdir}/GenomeBinning/MaxBin2/discarded" },
                 mode: params.publish_dir_mode,
                 pattern: '*.tooshort.gz'
-            ],
+            ]
         ]
         ext.prefix = { "${meta.assembler}-MaxBin2-${meta.id}" }
-        // if no gene found, will crash so allow ignore so rest of pipeline
-        // completes but without MaxBin2 results
     }
 
     withName: ADJUST_MAXBIN2_EXT {
@@ -642,11 +647,11 @@ process {
                 path: { "${params.outdir}/GenomeBinning/MaxBin2/bins/" },
                 mode: params.publish_dir_mode,
                 pattern: '*.fa.gz'
-            ],
+            ]
         ]
     }
 
-    withName: "CONCOCT_.*" {
+    withName: 'CONCOCT_.*' {
         publishDir = [
             [
                 path: { "${params.outdir}/GenomeBinning/CONCOCT/stats/" },
@@ -705,10 +710,10 @@ process {
                 path: { "${params.outdir}/GenomeBinning/DASTool" },
                 mode: params.publish_dir_mode,
                 pattern: '*.{tsv,log,eval,seqlength}'
-            ],
+            ]
         ]
         ext.prefix = { "${meta.assembler}-DASTool-${meta.id}" }
-        ext.args = "--write_bins --write_unbinned --write_bin_evals --score_threshold ${params.refine_bins_dastool_threshold}"
+        ext.args   = "--write_bins --write_unbinned --write_bin_evals --score_threshold ${params.refine_bins_dastool_threshold}"
     }
 
     withName: RENAME_POSTDASTOOL {
@@ -721,7 +726,6 @@ process {
             [
                 path: { "${params.outdir}/GenomeBinning/DASTool/bins" },
                 mode: params.publish_dir_mode,
-                // pattern needs to be updated in case of new binning methods
                 pattern: '*-{MetaBAT2,MaxBin2,CONCOCT}Refined-*.fa'
             ]
         ]
@@ -729,16 +733,16 @@ process {
 
     withName: TIARA_TIARA {
         publishDir = [
-                path: { "${params.outdir}/Taxonomy/Tiara/" },
-                mode: params.publish_dir_mode,
-                pattern: "*.txt"
-            ]
-        ext.args = { "--min_len ${params.tiara_min_length} --probabilities" }
+            path: { "${params.outdir}/Taxonomy/Tiara/" },
+            mode: params.publish_dir_mode,
+            pattern: "*.txt"
+        ]
+        ext.args   = { "--min_len ${params.tiara_min_length} --probabilities" }
         ext.prefix = { "${meta.assembler}-${meta.id}.tiara" }
     }
 
     withName: TIARA_CLASSIFY {
-        ext.args = { "--join_prokaryotes --assembler ${meta.assembler}" }
+        ext.args   = { "--join_prokaryotes --assembler ${meta.assembler}" }
         ext.prefix = { "${meta.assembler}-${meta.binner}-${meta.bin}-${meta.id}" }
     }
 
@@ -771,13 +775,12 @@ process {
         ]
     }
 
-    withName: 'MULTIQC' {
-        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
+    withName: MULTIQC {
+        ext.args   = { params.multiqc_title ? "--title \"${params.multiqc_title}\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
-
 }

From bfc2c0baf63c052d0fbed7174b165b6e24613d98 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Fri, 20 Sep 2024 14:54:46 +0200
Subject: [PATCH 18/24] Update CHANGELOG.md

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 31ae78bd..cf092806 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,7 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 
 - [#667](https://github.com/nf-core/mag/pull/667) - Fix pipeline crashing if only CONCOCT selected during binning (reported and fixed by @jfy133)
-- [#672](https://github.com/nf-core/mag/pull/672) - Fix GTDB-Tk per-sample TSV files not being published in output directory (reported by @jhayer, fix by @jfy133)
+- [#672](https://github.com/nf-core/mag/pull/673) - Fix GTDB-Tk per-sample TSV files not being published in output directory (reported by @jhayer, fix by @jfy133)
 
 ### `Dependencies`
 

From aa1f3d9996a47eb44b0334d2688d8bdb01064961 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Mon, 23 Sep 2024 18:09:57 +0000
Subject: [PATCH 19/24] Add exit code 12 to spades(hybrid), and standardise
 errorStrategy format

---
 CHANGELOG.md     |  1 +
 conf/base.config | 10 +++++-----
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index cf092806..ab0a3360 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Changed`
 
 - [#664](https://github.com/nf-core/mag/pull/664) - Update GTDBTk to latest version, with updated column names, update GTDB to release 220 (by @dialvarezs)
+- [#675](https://github.com/nf-core/mag/pull/675) - Added exit code 12 to valid SPAdes retry codes, due to OOM errors from spades-hammer (reported by @bawee, fix by @jfy133)
 
 ### `Fixed`
 
diff --git a/conf/base.config b/conf/base.config
index 2928a99b..839612ad 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -123,7 +123,7 @@ process {
         cpus          = { check_megahit_cpus (8, task.attempt  ) }
         memory        = { check_max (40.GB * task.attempt, 'memory' ) }
         time          = { check_max (16.h  * task.attempt, 'time'   ) }
-        errorStrategy = { task.exitStatus in [143,137,104,134,139,250] ? 'retry' : 'finish' }
+        errorStrategy = { task.exitStatus in ((130..145) + 104 + 250) ? 'retry' : 'finish' }
     }
     //SPAdes returns error(1) if it runs out of memory (and for other reasons as well...)!
     //exponential increase of memory and time with attempts, keep number of threads to enable reproducibility
@@ -131,14 +131,14 @@ process {
         cpus          = { check_spades_cpus (10, task.attempt) }
         memory        = { check_max (64.GB * (2**(task.attempt-1)), 'memory' ) }
         time          = { check_max (24.h  * (2**(task.attempt-1)), 'time'   ) }
-        errorStrategy = { task.exitStatus in [143,137,21,1] ? 'retry' : 'finish' }
+        errorStrategy = { task.exitStatus in ((130..145) + 104 + 12 + 21 + 12 + 1) ? 'retry' : 'finish' }
         maxRetries    = 5
     }
     withName: SPADESHYBRID {
         cpus          = { check_spadeshybrid_cpus (10, task.attempt) }
         memory        = { check_max (64.GB * (2**(task.attempt-1)), 'memory' ) }
         time          = { check_max (24.h  * (2**(task.attempt-1)), 'time'   ) }
-        errorStrategy = { task.exitStatus in [143,137,21,1] ? 'retry' : 'finish' }
+        errorStrategy = { task.exitStatus in ((130..145) + 104 + 12 + 21 + 12 + 1) ? 'retry' : 'finish' }
         maxRetries    = 5
     }
     //returns exit code 247 when running out of memory
@@ -146,7 +146,7 @@ process {
         cpus          = { check_max (2    * task.attempt, 'cpus'   ) }
         memory        = { check_max (8.GB * task.attempt, 'memory' ) }
         time          = { check_max (8.h  * task.attempt, 'time'   ) }
-        errorStrategy = { task.exitStatus in [143,137,104,134,139,247] ? 'retry' : 'finish' }
+        errorStrategy = { task.exitStatus in ((130..145) + 104 + 247) ? 'retry' : 'finish' }
     }
     withName: METABAT2_METABAT2 {
         cpus   = { check_max (8     * task.attempt, 'cpus'   ) }
@@ -168,6 +168,6 @@ process {
 
     withName: DASTOOL_DASTOOL {
         // if SCGs not found, bins cannot be assigned and DAS_tool will die with exit status 1
-        errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : task.exitStatus == 1 ? 'ignore' : 'finish' }
+        errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : task.exitStatus == 1 ? 'ignore' : 'finish' }
     }
 }

From 868cec1a830eb7f7000bb6f14581255214bf2149 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Tue, 24 Sep 2024 11:06:40 +0200
Subject: [PATCH 20/24] Apply suggestions from code review

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
---
 CHANGELOG.md     | 2 +-
 conf/base.config | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ab0a3360..d8bebe99 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Changed`
 
 - [#664](https://github.com/nf-core/mag/pull/664) - Update GTDBTk to latest version, with updated column names, update GTDB to release 220 (by @dialvarezs)
-- [#675](https://github.com/nf-core/mag/pull/675) - Added exit code 12 to valid SPAdes retry codes, due to OOM errors from spades-hammer (reported by @bawee, fix by @jfy133)
+- [#676](https://github.com/nf-core/mag/pull/676) - Added exit code 12 to valid SPAdes retry codes, due to OOM errors from spades-hammer (reported by @bawee, fix by @jfy133)
 
 ### `Fixed`
 
diff --git a/conf/base.config b/conf/base.config
index 839612ad..1e2540f3 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -131,14 +131,14 @@ process {
         cpus          = { check_spades_cpus (10, task.attempt) }
         memory        = { check_max (64.GB * (2**(task.attempt-1)), 'memory' ) }
         time          = { check_max (24.h  * (2**(task.attempt-1)), 'time'   ) }
-        errorStrategy = { task.exitStatus in ((130..145) + 104 + 12 + 21 + 12 + 1) ? 'retry' : 'finish' }
+        errorStrategy = { task.exitStatus in ((130..145) + 104 + 21 + 12 + 1) ? 'retry' : 'finish' }
         maxRetries    = 5
     }
     withName: SPADESHYBRID {
         cpus          = { check_spadeshybrid_cpus (10, task.attempt) }
         memory        = { check_max (64.GB * (2**(task.attempt-1)), 'memory' ) }
         time          = { check_max (24.h  * (2**(task.attempt-1)), 'time'   ) }
-        errorStrategy = { task.exitStatus in ((130..145) + 104 + 12 + 21 + 12 + 1) ? 'retry' : 'finish' }
+        errorStrategy = { task.exitStatus in ((130..145) + 104 + 21 + 12 + 1) ? 'retry' : 'finish' }
         maxRetries    = 5
     }
     //returns exit code 247 when running out of memory

From ce9e541cd7d7b6ddf80783707535105349334cd0 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 2 Oct 2024 13:42:41 +0200
Subject: [PATCH 21/24] Bump version for release

---
 CHANGELOG.md              | 4 ++--
 assets/multiqc_config.yml | 4 ++--
 nextflow.config           | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 76ac357c..d9c81bd1 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,12 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## dev [unreleased]
+## 3.1.0 [2024-10-02]
 
 ### `Added`
 
 - [#665](https://github.com/nf-core/mag/pull/648) - Add support for supplying pre-made bowtie host reference index (requested by @simone-pignotti, added by @jfy133)
-- [#670](https://github.com/nf-core/mag/pull/670) - Added --gtdbtk_pplacer_useram to run GTDBTk in memory mode rather than write to disk (reported by @harper357, fixed by @jfy133)
+- [#670](https://github.com/nf-core/mag/pull/670) - Added --gtdbtk_pplacer_useram to run GTDBTk in memory mode rather than write to disk (requested by @harper357, fixed by @jfy133)
 
 ### `Changed`
 
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 9f4e5e7e..8dcc79aa 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/mag/tree/dev" target="_blank">nf-core/mag</a>
+  This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/3.1.0" target="_blank">nf-core/mag</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/mag/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/mag/3.1.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-mag-methods-description":
     order: -1000
diff --git a/nextflow.config b/nextflow.config
index 3b43df33..312908fc 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -391,7 +391,7 @@ manifest {
     description     = """Assembly, binning and annotation of metagenomes"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '3.0.4dev'
+    version         = '3.1.0'
     doi             = '10.1093/nargab/lqac007'
 }
 

From 63ce1cb2238ddcfea0998e4668e50f78851281d3 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 2 Oct 2024 13:44:04 +0200
Subject: [PATCH 22/24] Harshil align

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 312908fc..2ea9d994 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -95,7 +95,7 @@ params {
     gtdbtk_min_perc_aa                   = 10
     gtdbtk_min_af                        = 0.65
     gtdbtk_pplacer_cpus                  = 1
-    gtdbtk_pplacer_useram            = false
+    gtdbtk_pplacer_useram                = false
 
     // long read preprocessing options
     skip_adapter_trimming                = false

From 375c018a396fc485bcd2cb501b89306f7f71bf46 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Thu, 3 Oct 2024 10:07:13 +0200
Subject: [PATCH 23/24] Apply suggestions from code review
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
---
 CHANGELOG.md         | 6 +++---
 nextflow_schema.json | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d9c81bd1..e08d2a9f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,12 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## 3.1.0 [2024-10-02]
+## 3.1.0 [2024-10-03]
 
 ### `Added`
 
 - [#665](https://github.com/nf-core/mag/pull/648) - Add support for supplying pre-made bowtie host reference index (requested by @simone-pignotti, added by @jfy133)
-- [#670](https://github.com/nf-core/mag/pull/670) - Added --gtdbtk_pplacer_useram to run GTDBTk in memory mode rather than write to disk (requested by @harper357, fixed by @jfy133)
+- [#670](https://github.com/nf-core/mag/pull/670) - Added `--gtdbtk_pplacer_useram` to run GTDBTk in memory mode rather than write to disk (requested by @harper357, fixed by @jfy133)
 
 ### `Changed`
 
@@ -29,7 +29,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Deprecated`
 
-- [#670](https://github.com/nf-core/mag/pull/670) - Deprecated --gtdbtk_pplacer_scratch due to unintuitive usage (reported by harper357, fixed by @jfy133)
+- [#670](https://github.com/nf-core/mag/pull/670) - Deprecated `--gtdbtk_pplacer_scratch` due to unintuitive usage (reported by harper357, fixed by @jfy133)
 
 ## 3.0.3 [2024-08-27]
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index dab2eb50..aaff9835 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -385,8 +385,8 @@
                 },
                 "host_fasta_bowtie2index": {
                     "type": "string",
-                    "description": "Bowtie2 index directory corresponding to --host_fasta reference file for host contamination removal.",
-                    "help_text": "This parameter must be used in combination with --host_fasta, and should be a directory containing files from the output of `bowtie2-build`, i.e. files ending in `.bt2`"
+                    "description": "Bowtie2 index directory corresponding to `--host_fasta` reference file for host contamination removal.",
+                    "help_text": "This parameter must be used in combination with `--host_fasta`, and should be a directory containing files from the output of `bowtie2-build`, i.e. files ending in `.bt2`"
                 },
                 "host_removal_verysensitive": {
                     "type": "boolean",

From a4d80ac704f7b1163b836863fd57a6f345866e6a Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Thu, 3 Oct 2024 16:08:27 +0200
Subject: [PATCH 24/24] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e08d2a9f..a80183c0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## 3.1.0 [2024-10-03]
+## 3.1.0 [2024-10-04]
 
 ### `Added`