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[skip ci] update pipeline tests for skip_qc
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‎tests/skip_qc.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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"GTF2BED": {
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"perl": "5.26.2"
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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
@@ -74,34 +74,34 @@
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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": "2024-10-10T11:17:30.991115"
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"timestamp": "2024-10-21T16:32:13.845479978"
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},
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"Params: --skip_qc": {
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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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"CUSTOM_GETCHROMSIZES": {
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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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"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"
@@ -119,22 +119,22 @@
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"picard": "3.1.1"
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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": 1.2
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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_STATS": {
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"samtools": 1.21
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"SE_GENE": {
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"bioconductor-summarizedexperiment": "1.32.0"
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"gawk": "5.1.0"
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"STRINGTIE_STRINGTIE": {
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"stringtie": "2.2.3"
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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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"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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"fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3",
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"fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
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"multiqc_citations.txt:md5,ef51c78faebdd32bad296ba14406b41e",
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"multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
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"multiqc_cutadapt.txt:md5,bc6ed9f59180b9346f22fb0f1e395dfa",
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"multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233",
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"multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f",
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"picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
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"cmd_info.json:md5,3a51e7db950cee84bed0b13e329f1934",
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"RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee",
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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": "2024-10-10T11:16:41.081492"
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"timestamp": "2024-10-21T16:31:26.493628799"
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}
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}
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}

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