From f05134e855e870086e1591d7423551baf57379eb Mon Sep 17 00:00:00 2001 From: Edmund Miller Date: Fri, 22 Jan 2021 11:49:24 -0600 Subject: [PATCH] ci: Add nextflow.log --- .github/workflows/bowtie_align.yml | 1 + .github/workflows/bowtie_index.yml | 1 + .github/workflows/bwa_index.yml | 1 + .github/workflows/bwa_mem.yml | 1 + .github/workflows/fastqc.yml | 1 + .github/workflows/gffread.yml | 1 + .github/workflows/multiqc.yml | 1 + .github/workflows/picard_collectmultiplemetrics.yml | 1 + .github/workflows/picard_markduplicates.yml | 1 + .github/workflows/picard_mergesamfiles.yml | 1 + .github/workflows/preseq_lcextrap.yml | 1 + .github/workflows/samtools_flagstat.yml | 1 + .github/workflows/samtools_idxstats.yml | 1 + .github/workflows/samtools_index.yml | 1 + .github/workflows/samtools_sort.yml | 1 + .github/workflows/samtools_stats.yml | 1 + .github/workflows/stringtie.yml | 1 + .github/workflows/trimgalore.yml | 1 + .github/workflows/ucsc_bedgraphtobigwig.yml | 1 + 19 files changed, 19 insertions(+) diff --git a/.github/workflows/bowtie_align.yml b/.github/workflows/bowtie_align.yml index 55c025d7..a5ac590c 100644 --- a/.github/workflows/bowtie_align.yml +++ b/.github/workflows/bowtie_align.yml @@ -47,5 +47,6 @@ jobs: with: name: logs path: | + /tmp/pytest_workflow_*/*/.nextflow.log /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/bowtie_index.yml b/.github/workflows/bowtie_index.yml index 93ff35df..cd1d7501 100644 --- a/.github/workflows/bowtie_index.yml +++ b/.github/workflows/bowtie_index.yml @@ -45,5 +45,6 @@ jobs: with: name: logs path: | + /tmp/pytest_workflow_*/*/.nextflow.log /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/bwa_index.yml b/.github/workflows/bwa_index.yml index 95395751..632dc5be 100644 --- a/.github/workflows/bwa_index.yml +++ b/.github/workflows/bwa_index.yml @@ -45,5 +45,6 @@ jobs: with: name: logs path: | + /tmp/pytest_workflow_*/*/.nextflow.log /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/bwa_mem.yml b/.github/workflows/bwa_mem.yml index af5290e5..2c5ccbcc 100644 --- a/.github/workflows/bwa_mem.yml +++ b/.github/workflows/bwa_mem.yml @@ -45,5 +45,6 @@ jobs: with: name: logs path: | + /tmp/pytest_workflow_*/*/.nextflow.log /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/fastqc.yml b/.github/workflows/fastqc.yml index 504e12ff..e9fae495 100644 --- a/.github/workflows/fastqc.yml +++ b/.github/workflows/fastqc.yml @@ -45,5 +45,6 @@ jobs: with: name: logs path: | + /tmp/pytest_workflow_*/*/.nextflow.log /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/gffread.yml b/.github/workflows/gffread.yml index 7509eafe..01ffa6c2 100644 --- a/.github/workflows/gffread.yml +++ b/.github/workflows/gffread.yml @@ -45,5 +45,6 @@ jobs: with: name: logs path: | + /tmp/pytest_workflow_*/*/.nextflow.log /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/multiqc.yml b/.github/workflows/multiqc.yml index 4070a1df..79d68e94 100644 --- a/.github/workflows/multiqc.yml +++ b/.github/workflows/multiqc.yml @@ -45,5 +45,6 @@ jobs: with: name: logs path: | + /tmp/pytest_workflow_*/*/.nextflow.log /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/picard_collectmultiplemetrics.yml b/.github/workflows/picard_collectmultiplemetrics.yml index 86130f75..84723c8a 100644 --- a/.github/workflows/picard_collectmultiplemetrics.yml +++ b/.github/workflows/picard_collectmultiplemetrics.yml @@ -45,5 +45,6 @@ jobs: with: name: logs path: | + /tmp/pytest_workflow_*/*/.nextflow.log /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/picard_markduplicates.yml b/.github/workflows/picard_markduplicates.yml index 5438d30b..ff6d7330 100644 --- a/.github/workflows/picard_markduplicates.yml +++ b/.github/workflows/picard_markduplicates.yml @@ -45,5 +45,6 @@ jobs: with: name: logs path: | + /tmp/pytest_workflow_*/*/.nextflow.log /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/picard_mergesamfiles.yml b/.github/workflows/picard_mergesamfiles.yml index aa8fa1a4..92568d10 100644 --- a/.github/workflows/picard_mergesamfiles.yml +++ b/.github/workflows/picard_mergesamfiles.yml @@ -45,5 +45,6 @@ jobs: with: name: logs path: | + /tmp/pytest_workflow_*/*/.nextflow.log /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/preseq_lcextrap.yml b/.github/workflows/preseq_lcextrap.yml index ea04bc8b..5dbb5369 100644 --- a/.github/workflows/preseq_lcextrap.yml +++ b/.github/workflows/preseq_lcextrap.yml @@ -45,5 +45,6 @@ jobs: with: name: logs path: | + /tmp/pytest_workflow_*/*/.nextflow.log /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/samtools_flagstat.yml b/.github/workflows/samtools_flagstat.yml index 3b2a956b..4c9f8396 100644 --- a/.github/workflows/samtools_flagstat.yml +++ b/.github/workflows/samtools_flagstat.yml @@ -45,5 +45,6 @@ jobs: with: name: logs path: | + /tmp/pytest_workflow_*/*/.nextflow.log /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/samtools_idxstats.yml b/.github/workflows/samtools_idxstats.yml index ffd4ce41..d3f544c7 100644 --- a/.github/workflows/samtools_idxstats.yml +++ b/.github/workflows/samtools_idxstats.yml @@ -45,5 +45,6 @@ jobs: with: name: logs path: | + /tmp/pytest_workflow_*/*/.nextflow.log /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/samtools_index.yml b/.github/workflows/samtools_index.yml index 74ea3e45..4bfde947 100644 --- a/.github/workflows/samtools_index.yml +++ b/.github/workflows/samtools_index.yml @@ -45,5 +45,6 @@ jobs: with: name: logs path: | + /tmp/pytest_workflow_*/*/.nextflow.log /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/samtools_sort.yml b/.github/workflows/samtools_sort.yml index 44b4bc12..45e7b563 100644 --- a/.github/workflows/samtools_sort.yml +++ b/.github/workflows/samtools_sort.yml @@ -45,5 +45,6 @@ jobs: with: name: logs path: | + /tmp/pytest_workflow_*/*/.nextflow.log /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/samtools_stats.yml b/.github/workflows/samtools_stats.yml index ba346e60..e3333d96 100644 --- a/.github/workflows/samtools_stats.yml +++ b/.github/workflows/samtools_stats.yml @@ -45,5 +45,6 @@ jobs: with: name: logs path: | + /tmp/pytest_workflow_*/*/.nextflow.log /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/stringtie.yml b/.github/workflows/stringtie.yml index d7bb6fff..6a9606a1 100644 --- a/.github/workflows/stringtie.yml +++ b/.github/workflows/stringtie.yml @@ -45,5 +45,6 @@ jobs: with: name: logs path: | + /tmp/pytest_workflow_*/*/.nextflow.log /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/trimgalore.yml b/.github/workflows/trimgalore.yml index 5bc54de5..392ced96 100644 --- a/.github/workflows/trimgalore.yml +++ b/.github/workflows/trimgalore.yml @@ -45,5 +45,6 @@ jobs: with: name: logs path: | + /tmp/pytest_workflow_*/*/.nextflow.log /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err diff --git a/.github/workflows/ucsc_bedgraphtobigwig.yml b/.github/workflows/ucsc_bedgraphtobigwig.yml index 935ad9aa..300df97c 100644 --- a/.github/workflows/ucsc_bedgraphtobigwig.yml +++ b/.github/workflows/ucsc_bedgraphtobigwig.yml @@ -44,5 +44,6 @@ jobs: with: name: logs path: | + /tmp/pytest_workflow_*/*/.nextflow.log /tmp/pytest_workflow_*/*/log.out /tmp/pytest_workflow_*/*/log.err