Merge pull request #94 from zifornd/pre-release-fixes-for-v1

pre-release fixes
nf-core · Oct 9, 2023 · 9fe10b0 · 9fe10b0
2 parents afef807 + b5f7341
commit 9fe10b0
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Showing 7 changed files with 57 additions and 7 deletions.
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,9 +1,9 @@
 report_comment: >
-  
+
   This report has been generated by the <a href="https://github.com/nf-core/rnasplice/releases/tag/1.0.0" target="_blank">nf-core/rnasplice</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/rnasplice/1.0.0/docs/output" target="_blank">documentation</a>.
-  
+
 report_section_order:
   "nf-core-rnasplice-methods-description":
     order: -1000

diff --git a/modules.json b/modules.json
@@ -22,7 +22,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "a33464f205fa15305bfe268546f6607b6f4d4753",
                         "installed_by": ["modules", "fastq_fastqc_umitools_trimgalore"]
                     },
                     "gffread": {
@@ -141,7 +141,7 @@
                     },
                     "fastq_fastqc_umitools_trimgalore": {
                         "branch": "master",
-                        "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
+                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
                         "installed_by": ["subworkflows"]
                     }
                 }

diff --git a/modules/local/dexseq_count.nf b/modules/local/dexseq_count.nf
@@ -5,7 +5,7 @@ process DEXSEQ_COUNT {
     conda "bioconda::htseq=2.0.2"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/htseq:2.0.2--py310ha14a713_0' :
-    'biocontainers/htseq:2.0.2--py310ha14a713_0' }"
+        'biocontainers/htseq:2.0.2--py310ha14a713_0' }"
 
     input:
     tuple val(meta), path(bam), path (gff)

diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test
diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap
diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/meta.yml b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/meta.yml
diff --git a/workflows/rnasplice.nf b/workflows/rnasplice.nf
@@ -756,7 +756,7 @@ workflow RNASPLICE {
         ch_multiqc_files = ch_multiqc_files.mix(FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_zip.collect{it[1]}.ifEmpty([]))
         ch_multiqc_files = ch_multiqc_files.mix(FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_log.collect{it[1]}.ifEmpty([]))
 
-        ch_multiqc_files = ch_fail_trimming_multiqc.collectFile(name: 'fail_trimmed_samples_mqc.tsv').ifEmpty([])
+        ch_multiqc_files = ch_multiqc_files.mix(ch_fail_trimming_multiqc.collectFile(name: 'fail_trimmed_samples_mqc.tsv').ifEmpty([]))
 
     }