Merge branch 'dev' into bwamem-fix

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

CHANGELOG.md

@@ -3,15 +3,15 @@
 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).
 
-## [dev]
+## [2.4.3] - 2022-03-24
 
 ### `Added`
 
 ### `Fixed`
 
 - [#828](https://github.com/nf-core/eager/issues/828) Improved error message if required metagenomic screening parameters not set correctly
 - [#836](https://github.com/nf-core/eager/issues/836) Remove deprecated parameters from test profiles
-- [#838](https://github.com/nf-core/eager/issues/836) Fix --snpcapture_bed files not being picked up by Nextflow (❤ to @meganemichel for reporting)
+- [#838](https://github.com/nf-core/eager/issues/838) Fix --snpcapture_bed files not being picked up by Nextflow (❤ to @meganemichel for reporting)
 - [#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
@@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#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)
 - [#858](https://github.com/nf-core/eager/pull/858) Corrected tutorials to reflect updated BAM trimming flags (❤ to @marcel-keller 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)
+- Corrected tutorials to reflect updated BAM trimming flags (❤ to @marcel-keller for reporting and correcting)
 
 ### `Dependencies`
 

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-2.4.3dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-eager-2.4.3/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-eager-2.4.3dev > nf-core-eager-2.4.3dev.yml
+RUN conda env export --name nf-core-eager-2.4.3 > nf-core-eager-2.4.3.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-2.4.3dev
+name: nf-core-eager-2.4.3
 channels:
   - conda-forge
   - bioconda
@@ -49,4 +49,4 @@ dependencies:
   - bioconda::eigenstratdatabasetools=1.0.2
   - bioconda::mapdamage2=2.2.1
   - bioconda::bbmap=38.92
-  - bioconda::bcftools=1.12
+  - bioconda::bcftools=1.12

main.nf

@@ -196,7 +196,7 @@ if("${params.fasta}".endsWith(".gz")){
     } else {
     fasta_for_indexing = Channel
     .fromPath("${params.fasta}", checkIfExists: true)
-    .into{ ch_fasta_for_bwaindex; ch_fasta_for_bt2index; ch_fasta_for_faidx; ch_fasta_for_seqdict; ch_fasta_for_circulargenerator; ch_fasta_for_circularmapper; ch_fasta_for_damageprofiler; ch_fasta_for_qualimap; ch_unmasked_fasta_for_masking; ch_unmasked_fasta_for_pmdtools; ch_fasta_for_genotyping_ug; ch_fasta__for_genotyping_hc; ch_fasta_for_genotyping_hc; ch_fasta_for_genotyping_freebayes; ch_fasta_for_genotyping_pileupcaller; ch_fasta_for_vcf2genome; ch_fasta_for_multivcfanalyzer;ch_fasta_for_genotyping_angsd;ch_fasta_for_damagerescaling;ch_fasta_for_bcftools_stats }
+    .into{ ch_fasta_for_bwaindex; ch_fasta_for_bt2index; ch_fasta_for_faidx; ch_fasta_for_seqdict; ch_fasta_for_circulargenerator; ch_fasta_for_circularmapper; ch_fasta_for_damageprofiler; ch_fasta_for_qualimap; ch_unmasked_fasta_for_masking; ch_unmasked_fasta_for_pmdtools; ch_fasta_for_genotyping_ug; ch_fasta__for_genotyping_hc; ch_fasta_for_genotyping_hc; ch_fasta_for_genotyping_freebayes; ch_fasta_for_genotyping_pileupcaller; ch_fasta_for_vcf2genome; ch_fasta_for_multivcfanalyzer; ch_fasta_for_genotyping_angsd; ch_fasta_for_damagerescaling; ch_fasta_for_bcftools_stats }
 }
 
 // Check that fasta index file path ends in '.fai'

nextflow.config

@@ -284,7 +284,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/eager:dev'
+process.container = 'nfcore/eager:2.4.3'
 
 // 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 = '2.4.3dev'
+  version = '2.4.3'
 }
 
 // Function to ensure that resource requirements don't go beyond