chore: Fix pipeline => nascent

nf-core · Dec 21, 2024 · 88e4d9e · 88e4d9e
1 parent 7a4e356
commit 88e4d9e
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Showing 21 changed files with 40 additions and 34 deletions.
diff --git a/workflows/tests/aligner/bowtie2.nf.test b/workflows/tests/aligner/bowtie2.nf.test
@@ -27,7 +27,7 @@ nextflow_pipeline {
                     // Number of tasks
                     workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
                     // All stable path name
                     stable_name,
                     // All files with stable contents

diff --git a/workflows/tests/aligner/bowtie2.nf.test.snap b/workflows/tests/aligner/bowtie2.nf.test.snap
@@ -172,7 +172,7 @@
                 "multiqc/multiqc_data/samtools_alignment_plot.txt",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
                 "preprocessing",
                 "preprocessing/fastp",
                 "preprocessing/fastp/cd4_REP1.trimmed.fastp.html",
@@ -324,4 +324,4 @@
         },
         "timestamp": "2024-12-18T07:25:45.87987"
     }
-}
+}
diff --git a/workflows/tests/aligner/bwa.nf.test b/workflows/tests/aligner/bwa.nf.test
@@ -28,7 +28,7 @@ nextflow_pipeline {
                     // Number of tasks
                     workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
                     // All stable path name
                     stable_name,
                     // All files with stable contents

diff --git a/workflows/tests/aligner/bwa.nf.test.snap b/workflows/tests/aligner/bwa.nf.test.snap
@@ -221,7 +221,7 @@
                 "multiqc/multiqc_data/samtools_alignment_plot.txt",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
                 "preprocessing",
                 "preprocessing/fastp",
                 "preprocessing/fastp/cd4_REP1.trimmed.fastp.html",
@@ -462,4 +462,4 @@
         },
         "timestamp": "2024-12-18T07:07:22.737667"
     }
-}
+}
diff --git a/workflows/tests/aligner/bwamem2.nf.test b/workflows/tests/aligner/bwamem2.nf.test
@@ -25,7 +25,7 @@ nextflow_pipeline {
                     // Number of tasks
                     workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
                     // All stable path name
                     stable_name,
                     // All files with stable contents

diff --git a/workflows/tests/aligner/bwamem2.nf.test.snap b/workflows/tests/aligner/bwamem2.nf.test.snap
@@ -186,7 +186,7 @@
                 "multiqc/multiqc_data/samtools_alignment_plot.txt",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
                 "preprocessing",
                 "preprocessing/fastp",
                 "preprocessing/fastp/cd4_REP1.trimmed.fastp.html",

diff --git a/workflows/tests/aligner/hisat2.nf.test b/workflows/tests/aligner/hisat2.nf.test
@@ -28,7 +28,7 @@ nextflow_pipeline {
                     // Number of tasks
                     workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
                     // All stable path name
                     stable_name,
                     // All files with stable contents

diff --git a/workflows/tests/aligner/hisat2.nf.test.snap b/workflows/tests/aligner/hisat2.nf.test.snap
@@ -187,7 +187,7 @@
                 "multiqc/multiqc_data/samtools_alignment_plot.txt",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
                 "preprocessing",
                 "preprocessing/fastp",
                 "preprocessing/fastp/cd4_REP1.trimmed.fastp.html",

diff --git a/workflows/tests/aligner/star.nf.test b/workflows/tests/aligner/star.nf.test
@@ -27,7 +27,7 @@ nextflow_pipeline {
                     // Number of tasks
                     workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
                     // All stable path name
                     stable_name,
                     // All files with stable contents
@@ -52,7 +52,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml")).match("gzip_software_versions") },
+                { assert snapshot(removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml")).match("gzip_software_versions") },
                 { assert snapshot(
                     workflow.trace.tasks().size(),
                 ).match()

diff --git a/workflows/tests/aligner/star.nf.test.snap b/workflows/tests/aligner/star.nf.test.snap
@@ -1,17 +1,17 @@
 {
     "Should run with gzipped gtf": {
         "content": [
-            93
+            98
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-12-21T11:57:47.575681"
+        "timestamp": "2024-11-25T21:02:16.647189"
     },
     "Should run with defaults": {
         "content": [
-            92,
+            97,
             {
                 "BBMAP_PILEUP": {
                     "bbmap": 39.01,
@@ -157,7 +157,7 @@
                 "multiqc/multiqc_data/samtools_alignment_plot.txt",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
                 "preprocessing",
                 "preprocessing/fastp",
                 "preprocessing/fastp/cd4_REP1.trimmed.fastp.html",
@@ -258,6 +258,9 @@
                 "star/samtools_stats/jurkat_genome.flagstat",
                 "star/samtools_stats/jurkat_genome.idxstats",
                 "star/samtools_stats/jurkat_genome.stats",
+                "star/samtools_stats/jurkat_transcriptome.flagstat",
+                "star/samtools_stats/jurkat_transcriptome.idxstats",
+                "star/samtools_stats/jurkat_transcriptome.stats",
                 "star/star",
                 "star/star/Genome",
                 "star/star/Log.out",
@@ -350,17 +353,20 @@
                 "jurkat_genome.flagstat:md5,b5f1d127de493e406882aced667210c9",
                 "jurkat_genome.idxstats:md5,5e4a68fda75c954324d659af58d12c62",
                 "jurkat_genome.stats:md5,5bf21e33fb56e0a38b53faf34b3be2ea",
+                "jurkat_transcriptome.flagstat:md5,2e10f27f80137c7ca4d340f110aa8fcf",
+                "jurkat_transcriptome.idxstats:md5,8e38ac91c083ef3c5cf77ba782b836a5",
+                "jurkat_transcriptome.stats:md5,322d7e620bcce35529aca042d0c8b3e8",
                 "Genome:md5,612664e3cfde5e1b73ad541d93752b31",
                 "SA:md5,074ae54177bb7b9cb981382f043f36e5",
-                "SAindex:md5,c8cae2d81bec99f68eddc0afe570090b",
+                "SAindex:md5,1c9cd646313f1abb1cfc205ccab73464",
                 "chrLength.txt:md5,b0be0a56ddefa84552742c72d4859eac",
                 "chrName.txt:md5,e99d7d1051eee43ceab5563c2d09fcee",
                 "chrNameLength.txt:md5,c985a141685e8431ec27c782816cb744",
                 "chrStart.txt:md5,6925b594ea2eeb964ba87cd6d42ab98f",
                 "exonGeTrInfo.tab:md5,ea42dd46e177f95a72a8f6a2925f7348",
                 "exonInfo.tab:md5,42a3ce2024f396b2298c0a84b07fb6e4",
                 "geneInfo.tab:md5,d0092fb1ea6fcdac270c4df788de70fb",
-                "genomeParameters.txt:md5,9e6f272d058d48c729d355ede94f8c87",
+                "genomeParameters.txt:md5,2fec04098057094f4b2e5a9ec4371a7d",
                 "sjdbInfo.txt:md5,12fb05dc7cea89735a0c19e1c0df61cb",
                 "sjdbList.fromGTF.out.tab:md5,5d9761b49920fb70a77d74e390d196b9",
                 "sjdbList.out.tab:md5,766fbca932681f8666b3a9e5fb3640bd",
@@ -380,7 +386,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-21T11:55:35.046966"
+        "timestamp": "2024-12-20T21:16:25.416797"
     },
     "gzip_software_versions": {
         "content": [
@@ -475,4 +481,4 @@
         },
         "timestamp": "2024-11-25T21:02:16.63526"
     }
-}
+}
diff --git a/workflows/tests/inputs/gff/main.nf.test b/workflows/tests/inputs/gff/main.nf.test
@@ -27,7 +27,7 @@ nextflow_pipeline {
                     // Number of tasks
                     workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
                     // All stable path name
                     stable_name,
                     // All files with stable contents

diff --git a/workflows/tests/inputs/gff/main.nf.test.snap b/workflows/tests/inputs/gff/main.nf.test.snap
@@ -171,7 +171,7 @@
                 "multiqc/multiqc_data/samtools_alignment_plot.txt",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
                 "preprocessing",
                 "preprocessing/fastp",
                 "preprocessing/fastp/cd4_REP1.trimmed.fastp.html",

diff --git a/workflows/tests/inputs/gzipped_gff/main.nf.test b/workflows/tests/inputs/gzipped_gff/main.nf.test
@@ -27,7 +27,7 @@ nextflow_pipeline {
                     // Number of tasks
                     workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
                     // All stable path name
                     stable_name,
                     // All files with stable contents

diff --git a/workflows/tests/inputs/gzipped_gff/main.nf.test.snap b/workflows/tests/inputs/gzipped_gff/main.nf.test.snap
@@ -171,7 +171,7 @@
                 "multiqc/multiqc_data/samtools_alignment_plot.txt",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
                 "preprocessing",
                 "preprocessing/fastp",
                 "preprocessing/fastp/cd4_REP1.trimmed.fastp.html",

diff --git a/workflows/tests/inputs/only_gff/main.nf.test b/workflows/tests/inputs/only_gff/main.nf.test
@@ -29,7 +29,7 @@ nextflow_pipeline {
                     // Number of tasks
                     workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
                     // All stable path name
                     stable_name,
                     // All files with stable contents

diff --git a/workflows/tests/inputs/only_gff/main.nf.test.snap b/workflows/tests/inputs/only_gff/main.nf.test.snap
@@ -174,7 +174,7 @@
                 "multiqc/multiqc_data/samtools_alignment_plot.txt",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
                 "preprocessing",
                 "preprocessing/fastp",
                 "preprocessing/fastp/cd4_REP1.trimmed.fastp.html",

diff --git a/workflows/tests/inputs/uniqmap/main.nf.test b/workflows/tests/inputs/uniqmap/main.nf.test
@@ -21,7 +21,7 @@ nextflow_pipeline {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml")).match("software_versions") },
+                { assert snapshot(removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml")).match("software_versions") },
                 // Files should have -uniqmap <directory> in the header
                 { assert path("$outputDir/transcript_identification/homer/cd4.bed").readLines()[18].contains("uniqMapDirectory = uniqmap.GRCh38_chr21.50nt") },
                 { assert path("$outputDir/transcript_identification/homer/cd4.bed").readLines()[20].contains("-uniqmap") },

diff --git a/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test b/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test
@@ -33,7 +33,7 @@ nextflow_pipeline {
                     // Number of tasks
                     workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
                     // All stable path name
                     stable_name,
                     // All files with stable contents

diff --git a/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test.snap b/workflows/tests/transcript_indentification/grohmm/only_gff/main.nf.test.snap
@@ -184,7 +184,7 @@
                 "multiqc/multiqc_data/samtools_alignment_plot.txt",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
                 "preprocessing",
                 "preprocessing/fastp",
                 "preprocessing/fastp/cd4_REP1.trimmed.fastp.html",
@@ -383,4 +383,4 @@
         },
         "timestamp": "2024-12-18T08:07:15.190593"
     }
-}
+}
diff --git a/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test b/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test
@@ -25,7 +25,7 @@ nextflow_pipeline {
                     // Number of tasks
                     workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml"),
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_nascent_software_mqc_versions.yml"),
                     // All stable path name
                     stable_name,
                     // All files with stable contents

diff --git a/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test.snap b/workflows/tests/transcript_indentification/grohmm/tuning/main.nf.test.snap
@@ -175,7 +175,7 @@
                 "multiqc/multiqc_data/samtools_alignment_plot.txt",
                 "multiqc/multiqc_report.html",
                 "pipeline_info",
-                "pipeline_info/nf_core_pipeline_software_mqc_versions.yml",
+                "pipeline_info/nf_core_nascent_software_mqc_versions.yml",
                 "preprocessing",
                 "preprocessing/fastp",
                 "preprocessing/fastp/cd4_REP1.trimmed.fastp.html",
@@ -374,4 +374,4 @@
         },
         "timestamp": "2024-12-18T08:25:02.333169"
     }
-}
+}