From 8554dc39b8375d0a1b42b033d52956e01142715c Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 2 Oct 2023 09:43:59 +0200 Subject: [PATCH 1/7] fix stringtie i/o --- subworkflows/local/stringtie_workflow.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/stringtie_workflow.nf b/subworkflows/local/stringtie_workflow.nf index d9e1c6c3..a2e427f4 100644 --- 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 From b6e651f9fbb675f36eb203ebea3ab9389f1e6012 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 2 Oct 2023 09:44:19 +0200 Subject: [PATCH 2/7] add stringtie to ci --- .github/workflows/ci.yml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e62dcf41..6a240bdb 100644 --- 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 }} From e1a56702cda0a52b2f6bc205cb994584d02cb6e8 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 2 Oct 2023 10:21:13 +0200 Subject: [PATCH 3/7] fix typo --- subworkflows/local/stringtie_workflow.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/stringtie_workflow.nf b/subworkflows/local/stringtie_workflow.nf index a2e427f4..e2ed99c4 100644 --- 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.map { meta, gtf -> [ gtf ]} + STRINGTIE_STRINGTIE(bam_sorted, ch_chrgtf.map { meta, gtf -> [ gtf ]) ch_versions = ch_versions.mix(STRINGTIE_STRINGTIE.out.versions) STRINGTIE_STRINGTIE From 1348ec7e6c65ab3e1f4b9b95301f850f1548d937 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 2 Oct 2023 10:35:59 +0200 Subject: [PATCH 4/7] fix typo --- subworkflows/local/stringtie_workflow.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/stringtie_workflow.nf b/subworkflows/local/stringtie_workflow.nf index e2ed99c4..a5872592 100644 --- 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.map { meta, gtf -> [ gtf ]) + STRINGTIE_STRINGTIE(bam_sorted, ch_chrgtf.map { meta, gtf -> [ gtf ]}) ch_versions = ch_versions.mix(STRINGTIE_STRINGTIE.out.versions) STRINGTIE_STRINGTIE From 8b46bbd0080f89acd6fa12037f6eace4e8d01b25 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 2 Oct 2023 11:18:46 +0200 Subject: [PATCH 5/7] fix channel i/o for stringtie merge --- subworkflows/local/stringtie_workflow.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/stringtie_workflow.nf b/subworkflows/local/stringtie_workflow.nf index a5872592..93a50e0c 100644 --- a/subworkflows/local/stringtie_workflow.nf +++ b/subworkflows/local/stringtie_workflow.nf @@ -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 } From 2cc2dc1a095ebd8f324ef7885e4e9d8225ae48f9 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 2 Oct 2023 13:23:29 +0200 Subject: [PATCH 6/7] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c192f932..c80769b7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ 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 ## v2.4.0 - [2023/09/22] From 8ece8421d10c4e968ad261af895f92699c6dde03 Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 2 Oct 2023 13:24:41 +0200 Subject: [PATCH 7/7] prettify --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c80769b7..0fb0b286 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ 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 ## v2.4.0 - [2023/09/22]