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nf-core · Oct 8, 2024 · 5c31fea · 5c31fea
1 parent 48337c8
commit 5c31fea
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Showing 3 changed files with 2 additions and 6 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -67,7 +67,6 @@ jobs:
           nf-test test \
               --ci \
               --shard ${{ matrix.shard }}/${{ env.SHARDS }} \
-              --changed-since HEAD^ \
               --profile "+${{ matrix.profile }}" \
               --filter pipeline \
               --junitxml=test.xml

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -43,7 +43,7 @@
                 },
                 "save_intermediates": {
                     "type": "boolean",
-                    "description": "Save all intermediate files (e.g. fastq, bams) to output directory",
+                    "description": "Save all intermediate files (e.g. fastq, bams) of all steps of the pipeline to output directory",
                     "fa_icon": "fas fa-save"
                 }
             }

diff --git a/subworkflows/local/mirna_quant.nf b/subworkflows/local/mirna_quant.nf
@@ -101,10 +101,7 @@ workflow MIRNA_QUANT {
             .map{ gtf, species -> [ [id:species.toString()], gtf, species ] }
             .collect()
 
-    BAM_STATS_MIRNA_MIRTOP(
-            BOWTIE_MAP_SEQCLUSTER.out.bam,
-            FORMAT_HAIRPIN.out.formatted_fasta,
-            ch_mirna_gtf_species )
+    BAM_STATS_MIRNA_MIRTOP(BOWTIE_MAP_SEQCLUSTER.out.bam, FORMAT_HAIRPIN.out.formatted_fasta, ch_mirna_gtf_species )
 
     ch_mirtop_logs = BAM_STATS_MIRNA_MIRTOP.out.stats_log
     ch_versions = ch_versions.mix(BAM_STATS_MIRNA_MIRTOP.out.versions)