Merge pull request #656 from nf-core/dev

Release PR for 3.0.3

CHANGELOG.md

@@ -3,6 +3,25 @@
 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).
 
+## 3.0.3 [2024-08-27]
+
+### `Added`
+
+### `Changed`
+
+### `Fixed`
+
+- [#648](https://github.com/nf-core/mag/pull/648) - Fix sample ID/assembly ID check failure when no IDs match (reported by @zackhenny, fix by @prototaxites)
+- [#646](https://github.com/nf-core/mag/pull/646) - GTDB-Tk directory input now creates a value channel so it runs for all entries to the process and not just the first (reported by @amizeranschi, fix by @prototaxites).
+- [#639](https://github.com/nf-core/mag/pull/639) - Fix pipeline failure when a sample produces only a single bin (fix by @d-callan)
+- [#651](https://github.com/nf-core/mag/pull/651) - Replace base container for bash only modules to reduce number of containers in pipeline (reported and fixed by @harper357)
+- [#652](https://github.com/nf-core/mag/pull/652) - Fix documentation typo in using user-defined assembly parameters (reported and fixed by @amizeranschi)
+- [#653](https://github.com/nf-core/mag/pull/653) - Fix overwriting of per-bin 'raw' GUNC RUN output files (multi-bin summary tables not affected) (reported by @zackhenny and fixed by @jfy133)
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## 3.0.2 [2024-07-04]
 
 ### `Added`

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) Hadrien Gourlé, Daniel Straub, Sabrina Krakau
+Copyright (c) Hadrien Gourlé, Daniel Straub, Sabrina Krakau, James A. Fellows Yates, Maxime Borry
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -77,14 +77,25 @@ When group-wise co-assembly is enabled, `SPAdes` is run on accordingly pooled re
 
 ## Credits
 
-nf-core/mag was written by [Hadrien Gourlé](https://hadriengourle.com) at [SLU](https://slu.se), [Daniel Straub](https://github.com/d4straub) and [Sabrina Krakau](https://github.com/skrakau) at the [Quantitative Biology Center (QBiC)](http://qbic.life). [James A. Fellows Yates](https://github.com/jfy133) and [Maxime Borry](https://github.com/maxibor) at the [Max Planck Institute for Evolutionary Anthropology](https://www.eva.mpg.de) joined in version 2.2.0. More recent contributors include [Jim Downie](https://github.com/prototaxites) and [Carson Miller](https://github.com/CarsonJM).
+nf-core/mag was written by [Hadrien Gourlé](https://hadriengourle.com) at [SLU](https://slu.se), [Daniel Straub](https://github.com/d4straub) and [Sabrina Krakau](https://github.com/skrakau) at the [Quantitative Biology Center (QBiC)](http://qbic.life). [James A. Fellows Yates](https://github.com/jfy133) and [Maxime Borry](https://github.com/maxibor) at the [Max Planck Institute for Evolutionary Anthropology](https://www.eva.mpg.de) joined in version 2.2.0.
+
+Other code contributors include:
+
+- [Antonia Schuster](https://github.com/AntoniaSchuster)
+- [Alexander Ramos](https://github.com/alxndrdiaz)
+- [Carson Miller](https://github.com/CarsonJM)
+- [Daniel Lundin](https://github.com/erikrikarddaniel)
+- [Danielle Callan](https://github.com/d-callan)
+- [Gregory Sprenger](https://github.com/gregorysprenger)
+- [Jim Downie](https://github.com/prototaxites)
+- [Phil Palmer](https://github.com/PhilPalmer)
+- [@willros](https://github.com/willros)
 
 Long read processing was inspired by [caspargross/HybridAssembly](https://github.com/caspargross/HybridAssembly) written by Caspar Gross [@caspargross](https://github.com/caspargross)
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
 - [Alexander Peltzer](https://github.com/apeltzer)
-- [Antonia Schuster](https://github.com/antoniaschuster)
 - [Phil Ewels](https://github.com/ewels)
 - [Gisela Gabernet](https://github.com/ggabernet)
 - [Harshil Patel](https://github.com/drpatelh)

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/3.0.2" target="_blank">nf-core/mag</a>
+  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>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/mag/3.0.2/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/mag/3.0.3/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-mag-methods-description":
     order: -1000

conf/base.config

@@ -58,10 +58,6 @@ process {
         maxRetries    = 2
     }
 
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
-
     withName: BOWTIE2_HOST_REMOVAL_BUILD {
         cpus   = { check_max (10    * task.attempt, 'cpus'   ) }
         memory = { check_max (20.GB * task.attempt, 'memory' ) }

conf/modules.config

@@ -447,7 +447,7 @@ process {
     // Make sure to keep directory in sync with gunc_qc.nf
     withName: 'GUNC_RUN' {
         publishDir = [
-            path: { "${params.outdir}/GenomeBinning/QC/GUNC/raw/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}" },
+            path: { "${params.outdir}/GenomeBinning/QC/GUNC/raw/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}/${fasta.baseName}/" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -456,7 +456,7 @@ process {
     // Make sure to keep directory in sync with gunc_qc.nf
     withName: 'GUNC_MERGECHECKM' {
         publishDir = [
-            path: { "${params.outdir}/GenomeBinning/QC/GUNC/checkmmerged/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}" },
+            path: { "${params.outdir}/GenomeBinning/QC/GUNC/checkmmerged/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}/${checkm_file.baseName}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]

docs/output.md

@@ -454,7 +454,7 @@ For each bin or refined bin the median sequencing depth is computed based on the
 - `GenomeBinning/depths/bins/`
   - `bin_depths_summary.tsv`: Summary of bin sequencing depths for all samples. Depths are available for samples mapped against the corresponding assembly, i.e. according to the mapping strategy specified with `--binning_map_mode`. Only for short reads.
   - `bin_refined_depths_summary.tsv`: Summary of sequencing depths for refined bins for all samples, if refinement was performed. Depths are available for samples mapped against the corresponding assembly, i.e. according to the mapping strategy specified with `--binning_map_mode`. Only for short reads.
-  - `[assembler]-[binner]-[sample/group]-binDepths.heatmap.png`: Clustered heatmap showing bin abundances of the assembly across samples. Bin depths are transformed to centered log-ratios and bins as well as samples are clustered by Euclidean distance. Again, sample depths are available according to the mapping strategy specified with `--binning_map_mode`.
+  - `[assembler]-[binner]-[sample/group]-binDepths.heatmap.png`: Clustered heatmap showing bin abundances of the assembly across samples. Bin depths are transformed to centered log-ratios and bins as well as samples are clustered by Euclidean distance. Again, sample depths are available according to the mapping strategy specified with `--binning_map_mode`. If a sample produces only a single bin, a heatmap will not be provided.
 
 </details>
 
@@ -565,9 +565,9 @@ If the parameter `--save_checkm_reference` is set, additionally the used the Che
 - `[gunc-database].dmnd`
 - `GUNC/`
   - `raw/`
-    - `[assembler]-[binner]-[domain]-[refinement]-[sample/group]/GUNC_checkM.merged.tsv`: Per sample GUNC [output](https://grp-bork.embl-community.io/gunc/output.html) containing with taxonomic and completeness QC statistics.
+    - `[assembler]-[binner]-[domain]-[refinement]-[sample/group]/[fasta input file name]/GUNC_checkM.merged.tsv`: Per sample GUNC [output](https://grp-bork.embl-community.io/gunc/output.html) containing with taxonomic and completeness QC statistics.
   - `checkmmerged/`
-    - `[assembler]-[binner]-[domain]-[refinement]-[sample/group]/GUNC.progenomes_2.1.maxCSS_level.tsv`: Per sample GUNC output merged with output from [CheckM](#checkm)
+    - `[assembler]-[binner]-[domain]-[refinement]-[sample/group]/[checkm input file name]/GUNC.progenomes_2.1.maxCSS_level.tsv`: Per sample GUNC output merged with output from [CheckM](#checkm)
 
 </details>
 

modules.json

@@ -87,11 +87,6 @@
                         "git_sha": "baa30accc6c50ea8a98662417d4f42ed18966353",
                         "installed_by": ["fasta_binning_concoct"]
                     },
-                    "custom/dumpsoftwareversions": {
-                        "branch": "master",
-                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
-                        "installed_by": ["modules"]
-                    },
                     "dastool/dastool": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",

modules/local/adjust_maxbin2_ext.nf

@@ -2,11 +2,10 @@ process ADJUST_MAXBIN2_EXT {
     tag "${meta.assembler}-${meta.id}"
     label 'process_low'
 
-    // Using container from multiqc since it'll be included anyway
-    conda "bioconda::multiqc=1.12"
+    conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'nf-core/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(bins)

modules/local/rename_postdastool.nf

@@ -2,11 +2,10 @@ process RENAME_POSTDASTOOL {
     tag "${meta.assembler}-${meta.id}"
     label 'process_low'
 
-    // Using container from multiqc since it'll be included anyway
-    conda "bioconda::multiqc=1.12"
+    conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'nf-core/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(bins)

modules/local/rename_predastool.nf

@@ -2,11 +2,10 @@ process RENAME_PREDASTOOL {
     tag "${meta.assembler}-${meta.binner}-${meta.id}"
     label 'process_low'
 
-    // Using container from multiqc since it'll be included anyway
-    conda "bioconda::multiqc=1.12"
+    conda "conda-forge::sed=4.7"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
-        'biocontainers/multiqc:1.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'nf-core/ubuntu:20.04' }"
 
     input:
     tuple val(meta), path(bins)