Merge pull request #416 from nf-core/fix_strintie_io

Fix strintie io
nf-core · Oct 2, 2023 · 91a5927 · 91a5927
2 parents c64830c + 8ece842
commit 91a5927
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Showing 3 changed files with 11 additions and 2 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -104,3 +104,10 @@ jobs:
           --outdir /home/runner/work/rnafusion/rnafusion/results --starfusion \
           --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \
           --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }}
+
+      - name: Dry test stingtie
+        run: |
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker -stub \
+          --outdir /home/runner/work/rnafusion/rnafusion/results --stringtie \
+          --genomes_base /home/runner/work/rnafusion/rnafusion/results/references \
+          --cosmic_username ${{ secrets.COSMIC_USERNAME }} --cosmic_passwd ${{ secrets.COSMIC_PASSWD }}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- Fix channel i/o issue in StringTie workflow and add StringTie in github CI tests [#416](https://github.com/nf-core/rnafusion/pull/416)
+
 ### Removed
 
 - Remove harsh trimming option `--trim` [#413](https://github.com/nf-core/rnafusion/pull/413)

diff --git a/subworkflows/local/stringtie_workflow.nf b/subworkflows/local/stringtie_workflow.nf
@@ -12,7 +12,7 @@ workflow STRINGTIE_WORKFLOW {
         ch_stringtie_gtf = Channel.empty()
 
         if ((params.stringtie || params.all) && !params.fusioninspector_only) {
-            STRINGTIE_STRINGTIE(bam_sorted, ch_chrgtf)
+            STRINGTIE_STRINGTIE(bam_sorted, ch_chrgtf.map { meta, gtf -> [ gtf ]})
             ch_versions = ch_versions.mix(STRINGTIE_STRINGTIE.out.versions)
 
             STRINGTIE_STRINGTIE
@@ -21,7 +21,7 @@ workflow STRINGTIE_WORKFLOW {
                 .map { it -> it[1] }
                 .set { stringtie_gtf }
 
-            STRINGTIE_MERGE ( stringtie_gtf, ch_chrgtf )
+            STRINGTIE_MERGE (stringtie_gtf, ch_chrgtf.map { meta, gtf -> [ gtf ]})
             ch_versions = ch_versions.mix(STRINGTIE_MERGE.out.versions)
             ch_stringtie_gtf = STRINGTIE_MERGE.out.gtf
         }