Merge pull request #875 from nf-core/dev

2.4.4 patch release

Author: jfy133

.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:2.4.3
+        run: docker build --no-cache . -t nfcore/eager:2.4.4
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/eager:dev
-          docker tag nfcore/eager:dev nfcore/eager:2.4.3
+          docker tag nfcore/eager:dev nfcore/eager:2.4.4
 
       - name: Install Nextflow
         env:

CHANGELOG.md

@@ -3,6 +3,18 @@
 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).
 
+## [2.4.4] - 2022-04-08
+
+### `Added`
+
+### `Fixed`
+
+- Fixed some auxiliary files (adapater list, snpcapture/pileupcaller/sexdeterrmine BED files, and pileupCaller SNP file, PMD reference mask) in some cases only be used against one sample (❤ to @meganemichel for reporting, fix by @jfy133)
+
+### `Dependencies`
+
+### `Deprecated`
+
 ## [2.4.3] - 2022-03-24
 
 ### `Added`
@@ -15,7 +27,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#843](https://github.com/nf-core/eager/issues/843) Re-add direct piping of AdapterRemovalFixPrefix to pigz
 - [#844](https://github.com/nf-core/eager/issues/844) Fixed reference masking prior to pmdtools
 - [#845](https://github.com/nf-core/eager/issues/845) Updates parameter documention to specify `-s` preseq parameter also applies to lc_extrap
-- [#851](https://github.com/nf-core/eager/issues/851) Fixes a file-name clash during additional_library_merge, post-BAM trimming of different UDG treated libraries of a sample
+- [#851](https://github.com/nf-core/eager/issues/851) Fixes a file-name clash during additional_library_merge, post-BAM trimming of different UDG treated libraries of a sample (❤ to @alexandregilardet for reporting)
 - Renamed a range of MultiQC general stats table headers to improve clarity, documentation has been updated accordingly
 - [#857](https://github.com/nf-core/eager/issues/857) Corrected samtools fastq flag to _retain_ read-pair information when converting off-target BAM files to fastq in paired-end mapping (❤ to @alexhbnr for reporting)
 - [#866](https://github.com/nf-core/eager/issues/866) Fixed a typo in the indexing step of BWA mem when not-collapsing (❤ to @alexhbnr for reporting)

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-2.4.3/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.4.4/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.4.3 > nf-core-eager-2.4.3.yml
+RUN conda env export --name nf-core-eager-2.4.4 > nf-core-eager-2.4.4.yml

environment.yml

@@ -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-2.4.3
+name: nf-core-eager-2.4.4
 channels:
   - conda-forge
   - bioconda

main.nf

@@ -238,45 +238,47 @@ if ( !params.clip_adapters_list ) {
     Channel
       .fromPath("$projectDir/assets/nf-core_eager_dummy2.txt", checkIfExists: true)
       .ifEmpty { exit 1, "[nf-core/eager] error: adapters list file not found. Please check input. Supplied: --clip_adapters_list '${params.clip_adapters_list}'." }
+      .collect()
       .set {ch_adapterlist}
 } else {
     Channel
       .fromPath("${params.clip_adapters_list}", checkIfExists: true)
       .ifEmpty { exit 1, "[nf-core/eager] error: adapters list file not found. Please check input. Supplied: --clip_adapters_list '${params.clip_adapters_list}'." }
+      .collect()
       .set {ch_adapterlist}
 }
 
 if ( params.snpcapture_bed ) {
-    Channel.fromPath(params.snpcapture_bed, checkIfExists: true).set { ch_snpcapture_bed }
+    ch_snpcapture_bed = Channel.fromPath(params.snpcapture_bed, checkIfExists: true).collect()
 } else {
-    Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt").set { ch_snpcapture_bed }
+    ch_snpcapture_bed = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt").collect()
 }
 
 // Set up channel with pmdtools reference mask bedfile
 if (!params.pmdtools_reference_mask) {
-  ch_bedfile_for_reference_masking = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt")
+  ch_bedfile_for_reference_masking = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt").collect()
 } else {
-  ch_bedfile_for_reference_masking = Channel.fromPath(params.pmdtools_reference_mask, checkIfExists: true)
+  ch_bedfile_for_reference_masking = Channel.fromPath(params.pmdtools_reference_mask, checkIfExists: true).collect()
 }
 
 // SexDetermination channel set up and bedfile validation
 if (!params.sexdeterrmine_bedfile) {
-  ch_bed_for_sexdeterrmine = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt")
+  ch_bed_for_sexdeterrmine = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt").collect()
 } else {
-  ch_bed_for_sexdeterrmine = Channel.fromPath(params.sexdeterrmine_bedfile, checkIfExists: true)
+  ch_bed_for_sexdeterrmine = Channel.fromPath(params.sexdeterrmine_bedfile, checkIfExists: true).collect()
 }
 
  // pileupCaller channel generation and input checks for 'random sampling' genotyping
 if (!params.pileupcaller_bedfile) {
-  ch_bed_for_pileupcaller = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt")
+  ch_bed_for_pileupcaller = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy.txt").collect()
 } else {
-  ch_bed_for_pileupcaller = Channel.fromPath(params.pileupcaller_bedfile, checkIfExists: true)
+  ch_bed_for_pileupcaller = Channel.fromPath(params.pileupcaller_bedfile, checkIfExists: true).collect()
 }
 
 if (!params.pileupcaller_snpfile) {
-  ch_snp_for_pileupcaller = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy2.txt")
+  ch_snp_for_pileupcaller = Channel.fromPath("$projectDir/assets/nf-core_eager_dummy2.txt").collect()
 } else {
-  ch_snp_for_pileupcaller = Channel.fromPath(params.pileupcaller_snpfile, checkIfExists: true)
+  ch_snp_for_pileupcaller = Channel.fromPath(params.pileupcaller_snpfile, checkIfExists: true).collect()
 }
 
 // Create input channel for MALT database directory, checking directory exists

nextflow.config

@@ -284,7 +284,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/eager:2.4.3'
+process.container = 'nfcore/eager:2.4.4'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -414,7 +414,7 @@ manifest {
   description = 'A fully reproducible and state-of-the-art ancient DNA analysis pipeline'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.07.1'
-  version = '2.4.3'
+  version = '2.4.4'
 }
 
 // Function to ensure that resource requirements don't go beyond
@@ -448,4 +448,4 @@ def check_max(obj, type) {
       return obj
     }
   }
-}
+}