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nf-core · Aug 1, 2024 · dd646af · dd646af
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Showing 6 changed files with 46 additions and 78 deletions.
diff --git a/workflows/tests/aligner/bowtie2.nf.test.snap b/workflows/tests/aligner/bowtie2.nf.test.snap
@@ -18,59 +18,27 @@
             ],
             "cd4.bed:md5,eae2a0135e62184e6117ced483b9cd9a",
             "jurkat.bed:md5,9255e426e272a406b3507847d4a57d5c",
-            [
-                "cd4_REP1.flagstat:md5,14e684e73cb41155ab1168a0a99a97e6",
-                "cd4_REP1.idxstats:md5,e32ac3215ba948bb7dd1559dab6c3c36",
-                "cd4_REP1.sorted.bam:md5,72a102c728e7fa3c30183de40304f982",
-                "cd4_REP1.sorted.bam.bai:md5,337d7333c37162ca7c29e314c792da18",
-                "cd4_REP1.stats:md5,490f84b5520b83daa95653671ce43921",
-                "cd4_REP2.flagstat:md5,e00d036bcbea6f944d45fb5cb7c34516",
-                "cd4_REP2.idxstats:md5,0803f2dce4b972ccc14943e22145c3e8",
-                "cd4_REP2.sorted.bam:md5,a6723653f41f23865c4cdf7e504d5c71",
-                "cd4_REP2.sorted.bam.bai:md5,034121901cf3ef98bc4aab6af347adfd",
-                "cd4_REP2.stats:md5,f8872ba7ef4b4e66b16a4ca3d63c1a65",
-                "cd4_REP3.flagstat:md5,5c1a10683eafbc0297795342a7f2da7d",
-                "cd4_REP3.idxstats:md5,02a44650c8a8837c1b049f33ee9700e4",
-                "cd4_REP3.sorted.bam:md5,82a37956f1e52684a2510677d003b3f6",
-                "cd4_REP3.sorted.bam.bai:md5,74fd9d808c006606f6117e1fcacfdc52",
-                "cd4_REP3.stats:md5,b97d9b383aed2bff197287e59028338d",
-                "cd4_REP4.flagstat:md5,9e02733772307969d1092ebabcdb7181",
-                "cd4_REP4.idxstats:md5,dc592aa507b946cef1a755067804e14b",
-                "cd4_REP4.sorted.bam:md5,680c31ed959079f4630e503a18626a0a",
-                "cd4_REP4.sorted.bam.bai:md5,b264afe2644d42f7b5c3b27c86d8f538",
-                "cd4_REP4.stats:md5,4abe0bd2ac90ded5782b408d5b77009d",
-                "jurkat_REP1.flagstat:md5,1b24ceabc8cecf34d745d06cf9d43cd0",
-                "jurkat_REP1.idxstats:md5,15e67d4d9d71c6cc6c37d5ce5414ede0",
-                "jurkat_REP1.sorted.bam:md5,f879712a966f60573c4595efcb3aba83",
-                "jurkat_REP1.sorted.bam.bai:md5,4be4a6032e17ec0ea826d56df890be4e",
-                "jurkat_REP1.stats:md5,f1bfa41900756241b62fcfb2e9ca1946",
-                "jurkat_REP2.flagstat:md5,a6ae93237077f1342a925961d2ef0d5f",
-                "jurkat_REP2.idxstats:md5,95d6840d5602f8c565fe566b791aa91e",
-                "jurkat_REP2.sorted.bam:md5,f9b0297821886923e16103c79f0cdea5",
-                "jurkat_REP2.sorted.bam.bai:md5,b58ddfb579c380c984d27b0f2cf3299c",
-                "jurkat_REP2.stats:md5,aa2aa377c5c045d7e077b9597ae49974"
-            ],
-            "ae7bc85e51ff0135fefa958006f1765f",
-            "f8b374b7fdb559c4a950730a58f5fc2a",
-            "72a32f7f67be6cc42b948af73dbd72f1",
-            "dc4823f7bf22b82600324e36366419cb",
-            "e84a653cc010046a62e362c8a053352",
-            "b57452295e8ca1ad8c1226ae6159a9f1"
+            "900325c1ad109ee12fa5f12c52f95b3f",
+            "c4e464e4c5f299c0fcb92d3e3ad856c1",
+            "35d5b2fbc71152546e7b6869986a3727",
+            "83171d18926d770e7accb0be6812a517",
+            "9b2f44262beeebcff3ccc103bb619894",
+            "4ccb14286f06945d7779e08b911501bd"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T16:34:20.592229077"
+        "timestamp": "2024-08-01T19:48:16.280408015"
     },
     "software_versions": {
         "content": [
-            "{Workflow={nf-core/nascent=v2.3.0dev}}"
+            "{BBMAP_PILEUP={bbmap=39.01, samtools=1.16.1, pigz=2.6}, BEDTOOLS_GENOMECOV_MINUS={bedtools=2.31.1}, BEDTOOLS_GENOMECOV_PLUS={bedtools=2.31.1}, BEDTOOLS_INTERSECT={bedtools=2.31.1}, BEDTOOLS_INTERSECT_FILTER={bedtools=2.31.1}, BOWTIE2_ALIGN={bowtie2=2.5.2, samtools=1.18, pigz=2.6}, DEEPTOOLS_BAMCOVERAGE_MINUS={deeptools=3.5.1}, DEEPTOOLS_BAMCOVERAGE_PLUS={deeptools=3.5.1}, FASTP={fastp=0.23.4}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, HOMER_MAKETAGDIRECTORY={homer=4.11, samtools=1.11}, PRESEQ_CCURVE={preseq=3.1.1}, PRESEQ_LCEXTRAP={preseq=3.1.1}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SUBREAD_FEATURECOUNTS_GENE={subread=2.0.1}, Workflow={nf-core/nascent=v2.3.0dev}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "23.10.4"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T17:33:38.038745876"
+        "timestamp": "2024-08-01T19:48:15.403043368"
     }
 }
diff --git a/workflows/tests/aligner/bwa.nf.test.snap b/workflows/tests/aligner/bwa.nf.test.snap
@@ -27,38 +27,38 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T17:52:04.533173666"
+        "timestamp": "2024-08-01T19:52:23.111205909"
     },
     "Should work with gzipped references": {
         "content": [
             98
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T17:54:56.153081188"
+        "timestamp": "2024-08-01T19:56:52.636381287"
     },
     "software_versions": {
         "content": [
-            "{BBMAP_PILEUP={bbmap=39.01, samtools=1.16.1, pigz=2.6}, BEDTOOLS_GENOMECOV_MINUS={bedtools=2.31.1}, BEDTOOLS_GENOMECOV_PLUS={bedtools=2.31.1}, BEDTOOLS_INTERSECT={bedtools=2.31.1}, BEDTOOLS_INTERSECT_FILTER={bedtools=2.31.1}, BWA_MEM={bwa=0.7.18-r1243-dirty, samtools=1.2}, DEEPTOOLS_BAMCOVERAGE_MINUS={deeptools=3.5.1}, DEEPTOOLS_BAMCOVERAGE_PLUS={deeptools=3.5.1}, FASTP={fastp=0.23.4}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, HOMER_MAKETAGDIRECTORY={homer=4.11, samtools=1.11}, PINTS_CALLER={python=3.10.6, pints=1.1.8}, PRESEQ_CCURVE={preseq=3.1.1}, PRESEQ_LCEXTRAP={preseq=3.1.1}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SUBREAD_FEATURECOUNTS_GENE={subread=2.0.1}, Workflow={nf-core/nascent=v2.3.0dev}}"
+            "{BBMAP_PILEUP={bbmap=39.01, samtools=1.16.1, pigz=2.6}, BEDTOOLS_GENOMECOV_MINUS={bedtools=2.31.1}, BEDTOOLS_GENOMECOV_PLUS={bedtools=2.31.1}, BEDTOOLS_INTERSECT={bedtools=2.31.1}, BEDTOOLS_INTERSECT_FILTER={bedtools=2.31.1}, BWA_MEM={bwa=0.7.18-r1243-dirty, samtools=1.2}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, DEEPTOOLS_BAMCOVERAGE_MINUS={deeptools=3.5.1}, DEEPTOOLS_BAMCOVERAGE_PLUS={deeptools=3.5.1}, FASTP={fastp=0.23.4}, FASTQC={fastqc=0.12.1}, HOMER_MAKETAGDIRECTORY={homer=4.11, samtools=1.11}, PINTS_CALLER={python=3.10.6, pints=1.1.8}, PRESEQ_CCURVE={preseq=3.1.1}, PRESEQ_LCEXTRAP={preseq=3.1.1}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SUBREAD_FEATURECOUNTS_GENE={subread=2.0.1}, Workflow={nf-core/nascent=v2.3.0dev}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T16:38:28.557110896"
+        "timestamp": "2024-08-01T19:52:22.661915581"
     },
     "Should work with BWA Index": {
         "content": [
             113
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T17:53:37.847333746"
+        "timestamp": "2024-08-01T19:54:47.955825977"
     }
 }
diff --git a/workflows/tests/aligner/bwamem2.nf.test.snap b/workflows/tests/aligner/bwamem2.nf.test.snap
@@ -27,18 +27,18 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T17:57:37.027770278"
+        "timestamp": "2024-08-01T19:59:55.730451885"
     },
     "software_versions": {
         "content": [
             "{BBMAP_PILEUP={bbmap=39.01, samtools=1.16.1, pigz=2.6}, BEDTOOLS_GENOMECOV_MINUS={bedtools=2.31.1}, BEDTOOLS_GENOMECOV_PLUS={bedtools=2.31.1}, BEDTOOLS_INTERSECT={bedtools=2.31.1}, BEDTOOLS_INTERSECT_FILTER={bedtools=2.31.1}, BWAMEM2_MEM={bwamem2=2.2.1, samtools=1.19.2}, DEEPTOOLS_BAMCOVERAGE_MINUS={deeptools=3.5.1}, DEEPTOOLS_BAMCOVERAGE_PLUS={deeptools=3.5.1}, FASTP={fastp=0.23.4}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, HOMER_MAKETAGDIRECTORY={homer=4.11, samtools=1.11}, PINTS_CALLER={python=3.10.6, pints=1.1.8}, PRESEQ_CCURVE={preseq=3.1.1}, PRESEQ_LCEXTRAP={preseq=3.1.1}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SUBREAD_FEATURECOUNTS_GENE={subread=2.0.1}, Workflow={nf-core/nascent=v2.3.0dev}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T16:42:18.575764822"
+        "timestamp": "2024-08-01T19:59:55.332896924"
     }
 }
diff --git a/workflows/tests/aligner/dragmap.nf.test.snap b/workflows/tests/aligner/dragmap.nf.test.snap
@@ -18,27 +18,27 @@
             ],
             "cd4.bed:md5,e9380700e48c1e52f76a2bb3fa4f59d9",
             "jurkat.bed:md5,fe88d4dc3c100262d7aec484e15b1c73",
-            "46f02dfa84368a95d905aaa0dc2196f9",
-            "8612e1d6ec11e2a1b4c7786922218301",
-            "889059858538de89fff9f23c0b2a3769",
-            "2e1d752974e0680a277f47e0df8fe214",
-            "1e43134d0e981a141728b27907b5da1f",
-            "d9d51702ce225c7fc5ecb06d69220678"
+            "54edc10bad3d380f2389f9a61b13a1c",
+            "9899ae3197a810e6f18e55caea424a99",
+            "328015578661fb01eeb6b03b82f14af4",
+            "39a98a35b0011dae7f6af96d4d306ce1",
+            "d76849b792c9246366f7bfd68ba52708",
+            "4bc4eebe2ef3d4f2d7d5b2571a684ec5"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T18:00:39.124238665"
+        "timestamp": "2024-08-01T20:04:35.189267908"
     },
     "software_versions": {
         "content": [
             "{BBMAP_PILEUP={bbmap=39.01, samtools=1.16.1, pigz=2.6}, BEDTOOLS_GENOMECOV_MINUS={bedtools=2.31.1}, BEDTOOLS_GENOMECOV_PLUS={bedtools=2.31.1}, BEDTOOLS_INTERSECT={bedtools=2.31.1}, BEDTOOLS_INTERSECT_FILTER={bedtools=2.31.1}, DEEPTOOLS_BAMCOVERAGE_MINUS={deeptools=3.5.1}, DEEPTOOLS_BAMCOVERAGE_PLUS={deeptools=3.5.1}, DRAGMAP_ALIGN={dragmap=1.2.1, samtools=1.15.1, pigz=2.3.4}, FASTP={fastp=0.23.4}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, HOMER_MAKETAGDIRECTORY={homer=4.11, samtools=1.11}, PINTS_CALLER={python=3.10.6, pints=1.1.8}, PRESEQ_CCURVE={preseq=3.1.1}, PRESEQ_LCEXTRAP={preseq=3.1.1}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SUBREAD_FEATURECOUNTS_GENE={subread=2.0.1}, Workflow={nf-core/nascent=v2.3.0dev}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T16:46:10.683659427"
+        "timestamp": "2024-08-01T20:04:34.724457691"
     }
 }
diff --git a/workflows/tests/aligner/hisat2.nf.test.snap b/workflows/tests/aligner/hisat2.nf.test.snap
@@ -21,24 +21,24 @@
             "7c6f110b93f069f6767d508f24e46986",
             "4b9dc03040268548300072c1ce32566f",
             "400f5f7f7744b7efa43a97c70a1d5359",
-            "d4b3f24ba300cfb911776de3d2e6538e",
+            "6d3a3f79144a0513ad93ffc27923ec5d",
             "d434e4ca752838ed82474bded157c92b",
-            "1b6d05586b36def8230dd51fb2a32bf9"
+            "b591522f5c8efb3bbd1b28ba64928c56"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T18:02:53.012401883"
+        "timestamp": "2024-08-01T20:07:42.799393547"
     },
     "software_versions": {
         "content": [
             "{BBMAP_PILEUP={bbmap=39.01, samtools=1.16.1, pigz=2.6}, BEDTOOLS_GENOMECOV_MINUS={bedtools=2.31.1}, BEDTOOLS_GENOMECOV_PLUS={bedtools=2.31.1}, BEDTOOLS_INTERSECT={bedtools=2.31.1}, BEDTOOLS_INTERSECT_FILTER={bedtools=2.31.1}, DEEPTOOLS_BAMCOVERAGE_MINUS={deeptools=3.5.1}, DEEPTOOLS_BAMCOVERAGE_PLUS={deeptools=3.5.1}, FASTP={fastp=0.23.4}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, HISAT2_ALIGN={hisat2=2.2.1, samtools=1.16.1}, HOMER_MAKETAGDIRECTORY={homer=4.11, samtools=1.11}, PINTS_CALLER={python=3.10.6, pints=1.1.8}, PRESEQ_CCURVE={preseq=3.1.1}, PRESEQ_LCEXTRAP={preseq=3.1.1}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SUBREAD_FEATURECOUNTS_GENE={subread=2.0.1}, UNTAR_HISAT2_INDEX={untar=1.34}, Workflow={nf-core/nascent=v2.3.0dev}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T16:49:23.757479838"
+        "timestamp": "2024-08-01T20:07:42.536938496"
     }
 }
diff --git a/workflows/tests/aligner/star.nf.test.snap b/workflows/tests/aligner/star.nf.test.snap
@@ -27,9 +27,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T19:00:10.008490733"
+        "timestamp": "2024-08-01T20:22:39.260502556"
     },
     "output_files": {
         "content": [
@@ -59,18 +59,18 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T18:07:31.331890729"
+        "timestamp": "2024-08-01T20:15:19.31686282"
     },
     "software_versions": {
         "content": [
             "{BBMAP_PILEUP={bbmap=39.01, samtools=1.16.1, pigz=2.6}, BEDTOOLS_GENOMECOV_MINUS={bedtools=2.31.1}, BEDTOOLS_GENOMECOV_PLUS={bedtools=2.31.1}, BEDTOOLS_INTERSECT={bedtools=2.31.1}, BEDTOOLS_INTERSECT_FILTER={bedtools=2.31.1}, DEEPTOOLS_BAMCOVERAGE_MINUS={deeptools=3.5.1}, DEEPTOOLS_BAMCOVERAGE_PLUS={deeptools=3.5.1}, FASTP={fastp=0.23.4}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, HOMER_MAKETAGDIRECTORY={homer=4.11, samtools=1.11}, PINTS_CALLER={python=3.10.6, pints=1.1.8}, PRESEQ_CCURVE={preseq=3.1.1}, PRESEQ_LCEXTRAP={preseq=3.1.1}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SUBREAD_FEATURECOUNTS_GENE={subread=2.0.1}, Workflow={nf-core/nascent=v2.3.0dev}}"
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.3"
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-31T16:56:37.229204359"
+        "timestamp": "2024-08-01T20:15:17.868733535"
     }
 }