Merge pull request #1052 from nf-core/patch-2.5.1

Patch 2.5.1

Author: TCLamnidis

.github/workflows/ci.yml

@@ -37,13 +37,13 @@ jobs:
 
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t nfcore/eager:2.5.0
+        run: docker build --no-cache . -t nfcore/eager:2.5.1
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/eager:dev
-          docker tag nfcore/eager:dev nfcore/eager:2.5.0
+          docker tag nfcore/eager:dev nfcore/eager:2.5.1
 
       - name: Install Nextflow
         env:

CHANGELOG.md

@@ -3,6 +3,22 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## [2.5.1] - 2024-02-21
+
+### `Added`
+
+- [#1037](https://github.com/nf-core/eager/issues/1037) Added an option to deactivate the `-sorted` option of bedtools coverage, in case the feature file is not sorted the same way as the fasta file, albeit with the caveat this will be very slow. (♥ Thanks to @IdoBar for reporting, and contributing.)
+
+### `Fixed`
+
+- [#1048](https://github.com/nf-core/eager/issues/1048) `--vcf2genome_outfile` parameter now gets prefixed by the sample_name and suffixed with `.fasta` (i.e. `<sample_name>_<vcf2genome_outfile>.fasta`). This ensures we avoid overwriting the output fasta of one sample with that of another when the option is provided. (♥ Thanks to @MeriamOs for reporting.)
+- [#1047](https://github.com/nf-core/eager/issues/1047) Changed the row some statistics were reported in the General Stats table. The File name collision fixed in 2.5.0 (see #1017) caused these statistics to be reported in the wrong row due to an added suffix.
+- [#1051](https://github.com/nf-core/eager/issues/1051) An error is now thrown if input BAM files end in `.unmapped.bam`, as this breaks the bam filtering process and empties the bam files in the process. (♥ Thanks to @PCQuilis for reporting.)
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## [2.5.0] - Bopfingen - 2023-11-03
 
 ### `Added`

Dockerfile

@@ -7,7 +7,7 @@ COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-eager-2.5.0/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.5.1/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.5.0 > nf-core-eager-2.5.0.yml
+RUN conda env export --name nf-core-eager-2.5.1 > nf-core-eager-2.5.1.yml

assets/multiqc_config.yaml

@@ -59,6 +59,8 @@ extra_fn_clean_exts:
   - ".trimmed_stats"
   - "_libmerged"
   - "_bt2"
+  - type: "regex"
+    pattern: "_udg(half|none|full)"
 
 top_modules:
   - "fastqc":

docs/images/usage/eager2_metromap_complex.png

@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-core-eager-2.5.0
+name: nf-core-eager-2.5.1
 channels:
   - conda-forge
   - bioconda

docs/images/usage/eager2_metromap_complex.svg

@@ -36,6 +36,11 @@ if ( params.bam && !params.single_end ) {
   exit 1, "[nf-core/eager] error: bams can only be specified with --single_end. Please check input command."
 }
 
+// Do not allow input bams to be suffixed with '.unmapped.bam'
+if (params.bam && params.input.endsWith('.unmapped.bam')) {
+  exit 1, "[nf-core/eager] error: Input BAM file names ending in '.unmapped.bam' are not allowed. Please rename your input BAM(s)."
+}
+
 // Validate that skip_collapse is only set to True for paired_end reads!
 if (!has_extension(params.input, "tsv") && params.skip_collapse  && params.single_end){
     exit 1, "[nf-core/eager] error: --skip_collapse can only be set for paired_end samples."
@@ -379,6 +384,9 @@ ch_input_sample_check
         def r2 = file(it[9]).getName()
         def bam = file(it[10]).getName()
 
+        // Throw error and exit if the input bam has a name ending in '.unmapped.bam'
+        if (bam.endsWith('.unmapped.bam')) { exit 1, "[nf-core/eager] error: Input BAM file names ending in '.unmapped.bam' are not allowed. Please rename your input BAM(s)." }
+
       [r1, r2, bam]
 
     }
@@ -2063,13 +2071,14 @@ process bedtools {
   tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*")
 
   script:
+  sorting_of_anno = params.anno_file_is_unsorted ? "" : "-sorted"
   """
   ## Create genome file from bam header
   samtools view -H ${bam} | grep '@SQ' | sed 's#@SQ\tSN:\\|LN:##g' > genome.txt
   
   ##  Run bedtools
-  bedtools coverage -nonamecheck -g genome.txt -sorted -a ${anno_file} -b ${bam} | pigz -p ${task.cpus - 1} > "${bam.baseName}".breadth.gz
-  bedtools coverage -nonamecheck -g genome.txt -sorted -a ${anno_file} -b ${bam} -mean | pigz -p ${task.cpus - 1} > "${bam.baseName}".depth.gz
+  bedtools coverage -nonamecheck -g genome.txt ${sorting_of_anno} -a ${anno_file} -b ${bam} | pigz -p ${task.cpus - 1} > "${bam.baseName}".breadth.gz
+  bedtools coverage -nonamecheck -g genome.txt ${sorting_of_anno} -a ${anno_file} -b ${bam} -mean | pigz -p ${task.cpus - 1} > "${bam.baseName}".depth.gz
   """
 }
 
@@ -2741,7 +2750,7 @@ process vcf2genome {
   tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, path("*.fasta.gz")
 
   script:
-  def out = !params.vcf2genome_outfile ? "${samplename}.fasta" : "${params.vcf2genome_outfile}"
+  def out = !params.vcf2genome_outfile ? "${samplename}.fasta" : "${samplename}_${params.vcf2genome_outfile}.fasta"
   def fasta_head = !params.vcf2genome_header ? "${samplename}" : "${params.vcf2genome_header}"
   """
   pigz -d -f -p ${task.cpus} ${vcf}