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[skip ci] First batch of pipeline test updates
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-192
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‎tests/default.nf.test.snap‎

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@@ -4,16 +4,16 @@
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{
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"BBMAP_BBSPLIT": {
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"bbmap": 39.01
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"bbmap": 39.1
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},
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"CAT_FASTQ": {
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"cat": 8.3
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"cat": 9.5
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},
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"CUSTOM_CATADDITIONALFASTA": {
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"python": null
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},
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"CUSTOM_GETCHROMSIZES": {
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"getchromsizes": 1.2
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"getchromsizes": 1.21
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},
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"FASTQC": {
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"fastqc": "0.12.1"
@@ -36,8 +36,8 @@
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"gawk": "5.1.0"
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},
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"TRIMGALORE": {
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"trimgalore": "0.6.7",
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"cutadapt": 3.4
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"trimgalore": "0.6.10",
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"cutadapt": 4.2
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},
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"UNTAR_SALMON_INDEX": {
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"untar": 1.34
@@ -88,31 +88,31 @@
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],
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"meta": {
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"nf-test": "0.9.0",
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"nextflow": "24.09.0"
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"nextflow": "24.04.4"
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},
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"timestamp": "2024-10-10T09:21:27.152841"
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"timestamp": "2024-10-21T15:18:53.239557126"
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},
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"Params: default": {
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"content": [
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{
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"BBMAP_BBSPLIT": {
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"bbmap": 39.01
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"bbmap": 39.1
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},
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"BEDTOOLS_GENOMECOV_FW": {
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},
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"CAT_FASTQ": {
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"cat": 8.3
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"cat": 9.5
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},
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"CUSTOM_CATADDITIONALFASTA": {
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"python": "3.9.5"
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"python": "3.12.2"
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},
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"CUSTOM_GETCHROMSIZES": {
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"getchromsizes": 1.2
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"getchromsizes": 1.21
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},
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"CUSTOM_TX2GENE": {
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"python": "3.9.5"
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"python": "3.10.4"
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},
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"DESEQ2_QC_PSEUDO": {
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"r-base": "4.0.3",
@@ -129,7 +129,7 @@
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"fastqc": "0.12.1"
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},
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"FQ_SUBSAMPLE": {
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"fq": "0.9.1 (2022-02-22)"
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"fq": "0.12.0 (2024-07-08)"
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},
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"GTF2BED": {
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"perl": "5.26.2"
@@ -174,22 +174,22 @@
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"rseqc": "5.0.2"
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},
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"SALMON_QUANT": {
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"salmon": "1.10.1"
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"salmon": "1.10.3"
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},
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"SAMTOOLS_FLAGSTAT": {
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"samtools": 1.2
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"samtools": 1.21
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},
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"SAMTOOLS_IDXSTATS": {
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"samtools": 1.2
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"samtools": 1.21
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},
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"SAMTOOLS_INDEX": {
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"samtools": 1.21
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},
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"SAMTOOLS_SORT": {
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"samtools": 1.21
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"samtools": 1.21
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},
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"SE_GENE": {
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"bioconductor-summarizedexperiment": "1.32.0"
@@ -205,14 +205,14 @@
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"gawk": "5.1.0"
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},
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"STRINGTIE_STRINGTIE": {
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"stringtie": "2.2.1"
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"stringtie": "2.2.3"
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},
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"SUBREAD_FEATURECOUNTS": {
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"subread": "2.0.1"
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"subread": "2.0.6"
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},
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"TRIMGALORE": {
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"trimgalore": "0.6.7",
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"cutadapt": 3.4
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"trimgalore": "0.6.10",
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"cutadapt": 4.2
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},
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"TXIMETA_TXIMPORT": {
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"bioconductor-tximeta": "1.20.1"
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"ucsc": 377
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"UCSC_BEDGRAPHTOBIGWIG": {
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"ucsc": 445
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"ucsc": 469
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},
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"UNTAR_SALMON_INDEX": {
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"untar": 1.34
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"RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217",
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"RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370",
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"RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043",
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"WT_REP1_intercept_slope.txt:md5,e7fcac6d125a7ba746a5cba4a1e66aef",
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"WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e",
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"RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,f3688a214d33a43ad79abe4b31df0c4b",
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"RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,6940e190bb388be56f282aa01e916466",
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"RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941",
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"RAP1_IAA_30M_REP1.featureCounts.txt:md5,b38da3230d4d29ebc8d4af36852d7212",
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"RAP1_IAA_30M_REP1.featureCounts.txt:md5,2a5c8c10f4371048d7d459411b58b087",
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"RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,d241d50e582ceb97e6f16b3556f5f5a9",
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"RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb",
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"RAP1_UNINDUCED_REP1.featureCounts.txt:md5,2ab175746532de1c54020c1eabc27bb5",
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"RAP1_UNINDUCED_REP1.featureCounts.txt:md5,a8ad2573b09fbef181d2d5792a74dbd4",
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"RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0",
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"RAP1_UNINDUCED_REP2.featureCounts.txt:md5,480b2586a878bc22f5b73f94051b41d8",
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"WT_REP1.biotype_counts_mqc.tsv:md5,cac41767a8cc2e5fee58637971ec89d1",
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"RAP1_UNINDUCED_REP2.featureCounts.txt:md5,c97046671b304b69811872854c361450",
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"WT_REP1.biotype_counts_mqc.tsv:md5,e0dbe5dcff076b97775677fd64b29b04",
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"WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9",
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"WT_REP1.featureCounts.txt:md5,112001ddbe917d935ee276d1685840bd",
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"WT_REP2.biotype_counts_mqc.tsv:md5,e61b72317ac3c4d4ac64b663145e6262",
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"WT_REP1.featureCounts.txt:md5,b2a80018f38c142a936e8ad5d24059f8",
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"WT_REP2.biotype_counts_mqc.tsv:md5,5cb8f29f175d07b3d8f8464bf8fcd82b",
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"WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481",
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"WT_REP2.featureCounts.txt:md5,59e23ae18cfe6aa2e5a884bc03cbff15",
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"RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee",
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"RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8",
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"RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033",
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],
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"meta": {
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"nf-test": "0.9.0",
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"nextflow": "24.09.0"
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"nextflow": "24.04.4"
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},
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"timestamp": "2024-10-10T09:48:14.477734"
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"timestamp": "2024-10-21T15:17:50.647397994"
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}
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}
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}

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