Merge pull request sanger-tol#90 from sanger-tol/pacbio_fix

Fix when multiple PacBio files are given

.github/workflows/branch.yml

@@ -1,15 +1,15 @@
 name: nf-core branch protection
-# This workflow is triggered on PRs to master branch on the repository
-# It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev`
+# This workflow is triggered on PRs to main branch on the repository
+# It fails when someone tries to make a PR against the nf-core `main` branch instead of `dev`
 on:
   pull_request_target:
-    branches: [master]
+    branches: [main]
 
 jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
+      # PRs to the nf-core repo main branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
         if: github.repository == 'sanger-tol/readmapping'
         run: |
@@ -22,7 +22,7 @@ jobs:
         uses: mshick/add-pr-comment@v1
         with:
           message: |
-            ## This PR is against the `master` branch :x:
+            ## This PR is against the `main` branch :x:
 
             * Do not close this PR
             * Click _Edit_ and change the `base` to `dev`
@@ -32,9 +32,9 @@ jobs:
 
             Hi @${{ github.event.pull_request.user.login }},
 
-            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch.
-            The `master` branch on nf-core repositories should always contain code from the latest release.
-            Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
+            It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `main` branch.
+            The `main` branch on nf-core repositories should always contain code from the latest release.
+            Because of this, PRs to `main` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch.
 
             You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page.
             Note that even after this, the test will continue to show as failing until you push a new commit.

.nf-core.yml

@@ -18,6 +18,7 @@ lint:
     - assets/sendmail_template.txt
     - docs/README.md
     - lib/NfcoreTemplate.groovy
+    - .github/workflows/branch.yml
   nextflow_config:
     - manifest.name
     - manifest.homePage

CHANGELOG.md

@@ -3,7 +3,13 @@
 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).
 
-## [[1.2.1](https://github.com/sanger-tol/readmapping/releases/tag/1.2.1)] - [2024-02-29]
+## [[1.2.2](https://github.com/sanger-tol/readmapping/releases/tag/1.2.2)] - Norwegian Ridgeback (patch 2) -[2024-05-23]
+
+### Enhancements & fixes
+
+- Fixed the bug in the filtering of multiple PacBio files
+
+## [[1.2.1](https://github.com/sanger-tol/readmapping/releases/tag/1.2.1)] - Norwegian Ridgeback (patch 1) - [2024-02-29]
 
 ### Enhancements & fixes
 

assets/samplesheet.csv

@@ -3,3 +3,5 @@ mMelMel1,illumina,/lustre/scratch123/tol/resources/nextflow/test-data/Meles_mele
 mMelMel2,illumina,/lustre/scratch123/tol/resources/nextflow/test-data/Meles_meles/genomic_data/mMelMel2/illumina/31231_4#1.subset.cram,
 mMelMel3,hic,/lustre/scratch123/tol/resources/nextflow/test-data/Meles_meles/genomic_data/mMelMel3/hic/35528_2#1.subset.cram,
 mMelMel3,ont,/lustre/scratch123/tol/resources/nextflow/test-data/Meles_meles/genomic_data/mMelMel3/ont/PAE35587_pass_1f1f0707_115.subset.fastq.gz,
+mMelMel3,pacbio,/lustre/scratch123/tol/resources/nextflow/test-data/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200910_173211.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.bam,
+mMelMel3,pacbio,/lustre/scratch123/tol/resources/nextflow/test-data/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.bam,

assets/samplesheet_s3.csv

@@ -3,3 +3,5 @@ mMelMel1,illumina,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_d
 mMelMel2,illumina,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel2/illumina/31231_4%231.subset.cram,
 mMelMel3,hic,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/hic/35528_2%231.subset.cram,
 mMelMel3,ont,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/ont/PAE35587_pass_1f1f0707_115.subset.fastq.gz,
+mMelMel3,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200910_173211.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.bam,
+mMelMel3,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.bam,

modules/local/pacbio_filter.nf

@@ -11,8 +11,8 @@ process PACBIO_FILTER {
     tuple val(meta), path(txt)
 
     output:
-    path("*.blocklist"),  emit: list
-    path  "versions.yml", emit: versions
+    tuple val(meta), path("*.blocklist"), emit: list
+    path  "versions.yml"                , emit: versions
 
     when:
     task.ext.when == null || task.ext.when

nextflow.config

@@ -183,7 +183,7 @@ manifest {
     description     = 'Pipeline to map reads generated using different sequencing technologies against a genome assembly.'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.2.1'
+    version         = '1.2.2'
     doi             = '10.5281/zenodo.6563577'
 }
 

subworkflows/local/filter_pacbio.nf

@@ -60,9 +60,18 @@ workflow FILTER_PACBIO {
     // Create filtered BAM file
     SAMTOOLS_CONVERT.out.bam
     | join ( SAMTOOLS_CONVERT.out.csi )
+    | join ( PACBIO_FILTER.out.list )
+    | set { ch_reads_and_list }
+
+    ch_reads_and_list
+    | map { meta, bam, csi, list -> [meta, bam, csi] }
     | set { ch_reads }
 
-    SAMTOOLS_FILTER ( ch_reads, [ [], [] ], PACBIO_FILTER.out.list )
+    ch_reads_and_list
+    | map { meta, bam, csi, list -> list }
+    | set { ch_lists }
+
+    SAMTOOLS_FILTER ( ch_reads, [ [], [] ], ch_lists )
     ch_versions = ch_versions.mix ( SAMTOOLS_FILTER.out.versions.first() )