Merge pull request #70 from nf-core/dev

chore: release 1.0.1

CHANGELOG.md

@@ -3,7 +3,26 @@
 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).
 
-## [[1.0.0]](https://github.com/nf-core/fastquorum/releases/tag/1.0.0)] -- 2024-05-20
+## [[1.0.1]](https://github.com/nf-core/fastquorum/releases/tag/1.0.1) -- 2024-09-10
+
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Nils Homer](https://github.com/nh13)
+- [Simon Pearce](https://github.com/SPPearce)
+- [Zach Norgaard](https://github.com/znorgaard)
+
+### Enhancements & fixes
+
+- [PR #51](https://github.com/nf-core/fastquorum/pull/51) - Fixes a bug where alignment and filtering where swapped in the phase 2 high-throughput diagrams (@jfy133).
+- [PR #58](https://github.com/nf-core/fastquorum/pull/58) - Prepare genome steps now run only if the corresponding parameters are not passed.
+- [PR #60](https://github.com/nf-core/fastquorum/pull/60) - Enable automatic escalation of memory for FilterConsensusReads.
+- [PR #67](https://github.com/nf-core/fastquorum/pull/67) - Fix setting the parameters from igenomes.
+- [PR #68](https://github.com/nf-core/fastquorum/pull/68) - Temporary fix to merging BAMs across lanes in template-coordinate order. Using `fgbio SortBam` after `samtools merge`. Related to [samtools#2062](https://github.com/samtools/samtools/pull/2062).
+- [PR #71](https://github.com/nf-core/fastquorum/pull/71) - Add stubs to all local modules.
+
+## [[1.0.0]](https://github.com/nf-core/fastquorum/releases/tag/1.0.0) -- 2024-05-20
 
 Initial release of nf-core/fastquorum, created with the [nf-core](https://nf-co.re/) template.
 

README.md

@@ -6,9 +6,8 @@
 </h1>
 
 [![GitHub Actions CI Status](https://github.com/nf-core/fastquorum/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/fastquorum/actions/workflows/ci.yml)
-[![GitHub Actions Linting Status](https://github.com/nf-core/fastquorum/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/fastquorum/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/fastquorum/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![GitHub Actions Linting Status](https://github.com/nf-core/fastquorum/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/fastquorum/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/fastquorum/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.11267672-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.11267672)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
-
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
@@ -152,10 +151,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-If you use nf-core/fastquorum for your analysis, please cite for this pipeline and [![DOI](https://zenodo.org/badge/53011104.svg)](https://zenodo.org/doi/10.5281/zenodo.10456900) for [`fgbio`](https://github.com/fulcrumgenomics/fgbio).
-
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use nf-core/fastquorum for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+If you use nf-core/fastquorum for your analysis, please cite [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.11267672.svg)](https://doi.org/10.5281/zenodo.11267672) for this pipeline and [![DOI](https://zenodo.org/badge/53011104.svg)](https://zenodo.org/doi/10.5281/zenodo.10456900) for [`fgbio`](https://github.com/fulcrumgenomics/fgbio).
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/fastquorum/releases/tag/1.0.0" target="_blank">nf-core/fastquorum</a>
+  This report has been generated by the <a href="https://github.com/nf-core/fastquorum/releases/tag/1.0.1" target="_blank">nf-core/fastquorum</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/fastquorum/1.0.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/fastquorum/1.0.1/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-fastquorum-methods-description":
     order: -1000

conf/base.config

@@ -21,11 +21,6 @@ process {
     maxErrors     = '-1'
 
     // Process-specific resource requirements
-    // NOTE - Please try and re-use the labels below as much as possible.
-    //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
-    //        If possible, it would be nice to keep the same label naming convention when
-    //        adding in your local modules too.
-    // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
         cpus   = { check_max( 1                  , 'cpus'    ) }
         memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
@@ -59,12 +54,4 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName:'FASTQC'{
-        cpus   = { check_max( 4 * task.attempt, 'cpus' ) }
-        memory = { check_max( 4.GB * task.attempt, 'memory' ) }
-    }
-    withName:'MULTIQC' {
-        cpus   = { check_max( 4 * task.attempt, 'cpus' ) }
-        memory = { check_max( 12.GB * task.attempt, 'memory' ) }
-    }
 }

conf/igenomes.config

@@ -13,6 +13,8 @@ params {
     genomes {
         'GRCh37' {
             fasta       = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa"
+            fasta_fai   = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa.fai"
+            dict        = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.dict"
             bwa         = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/"
             bowtie2     = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/"
             star        = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/"
@@ -26,6 +28,8 @@ params {
         }
         'GRCh38' {
             fasta       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
+            fasta_fai   = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa.fai"
+            dict        = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.dict"
             bwa         = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/"
             bowtie2     = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/"
             star        = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/"

conf/modules.config

@@ -18,7 +18,26 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    withName: 'BWA_INDEX|SAMTOOLS_FAIDX|SAMTOOLS_DICT' {
+    withName: 'BWA_INDEX' {
+        ext.when = { !params.bwa }
+        publishDir = [
+            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
+        ]
+    }
+
+    withName: 'SAMTOOLS_FAIDX' {
+        ext.when = { !params.fasta_fai }
+        publishDir = [
+            path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> (filename != 'versions.yml' && params.save_reference) ? filename : null }
+        ]
+    }
+
+    withName: 'SAMTOOLS_DICT' {
+        ext.when = { !params.dict }
         publishDir = [
             path: { params.save_reference ? "${params.outdir}/genome" : params.outdir },
             mode: params.publish_dir_mode,
@@ -27,6 +46,8 @@ process {
     }
 
     withName: 'FASTQC' {
+        cpus   = { check_max( 4 * task.attempt, 'cpus' ) }
+        memory = { check_max( 4.GB * task.attempt, 'memory' ) }
         ext.args = '--quiet'
         publishDir = [
             path: { "${params.outdir}/preprocessing/fastqc/${meta.id}" },
@@ -67,6 +88,17 @@ process {
         ]
     }
 
+    /* This can be removed when https://github.com/samtools/samtools/pull/2062 is merged */
+    withName: '.*SORTBAM' {
+        ext.args = '--sort-order TemplateCoordinate'
+        ext.prefix = { "${meta.id}.sorted" }
+        publishDir = [
+            path: { "${params.outdir}/preprocessing/merged/${meta.id}" },
+            mode: params.publish_dir_mode,
+            pattern: '*.bam'
+        ]
+    }
+
     withName: '.*GROUPREADSBYUMI' {
         publishDir = [
             [
@@ -107,10 +139,6 @@ process {
         ]
     }
 
-    withName: '.*FILTERCONSENSUSREADS' {
-        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }
-    }
-
     withName: '.*CALLANDFILTERDUPLEXCONSENSUSREADS|.*CALLANDFILTERMOLECULARCONSENSUSREADS|.*FILTERCONSENSUSREADS' {
         publishDir = [
             [
@@ -126,6 +154,10 @@ process {
         ]
     }
 
+    withName:'FILTERCONSENSUSREADS' {
+        memory = { check_max( 12.GB * task.attempt, 'memory' ) }
+    }
+
     withName: '.*ALIGN_CONSENSUS_BAM' {
         publishDir = [
             path: { "${params.outdir}/filtering/align_consensus_bam/${meta.id}" },
@@ -135,6 +167,8 @@ process {
     }
 
     withName: 'MULTIQC' {
+        cpus   = { check_max( 4 * task.attempt, 'cpus' ) }
+        memory = { check_max( 12.GB * task.attempt, 'memory' ) }
         ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc" },
@@ -143,5 +177,4 @@ process {
         ]
     }
 
-
 }