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edmundmilleredmundmiller
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build: Rename arm profile to apple and make a real arm profile
Update container versions for ARM architecture and
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‎conf/containers/containers_docker_arm64.config

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process { withName: 'BBMAP_BBSPLIT' { container = 'community.wave.seqera.io/library/bbmap:39.10--168578230ff6490a' } }
2-
process { withName: 'BEDTOOLS_GENOMECOV' { container = 'community.wave.seqera.io/library/bedtools:2.31.1--7c4ce4cb07c09ee4' } }
3-
process { withName: 'BRACKEN_BRACKEN' { container = 'community.wave.seqera.io/library/bracken:2.9--3d5af74ed6966fc1' } }
4-
process { withName: 'CAT_FASTQ' { container = 'community.wave.seqera.io/library/coreutils:9.5--ae99c88a9b28c264' } }
5-
process { withName: 'CUSTOM_CATADDITIONALFASTA' { container = 'community.wave.seqera.io/library/python:3.12.2--8aba3d9ac529ff19' } }
6-
process { withName: 'CUSTOM_GETCHROMSIZES' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } }
7-
process { withName: 'CUSTOM_TX2GENE' { container = 'community.wave.seqera.io/library/python:3.10.4--a643e28963f01eef' } }
8-
process { withName: 'DESEQ2_QC' { container = 'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:d06fadc02f8422a2' } }
9-
process { withName: 'DUPRADAR' { container = 'community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--dcb3a3be56be6612' } }
10-
process { withName: 'FASTP' { container = 'community.wave.seqera.io/library/fastp:0.23.4--f8cefc1e5f7a782e' } }
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process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--af7a5314d5015c29' } }
12-
process { withName: 'FQ_LINT' { container = 'community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } }
13-
process { withName: 'FQ_SUBSAMPLE' { container = 'community.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa' } }
14-
process { withName: 'GFFREAD' { container = 'community.wave.seqera.io/library/gffread:0.12.7--33b95f1cfcc0e572' } }
15-
process { withName: 'GTF2BED' { container = 'community.wave.seqera.io/library/perl:5.26.2--e6570c5f08d3e12c' } }
16-
process { withName: 'GTF_FILTER' { container = 'community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } }
17-
process { withName: 'GUNZIP' { container = 'community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } }
18-
process { withName: 'HISAT2_ALIGN' { container = 'community.wave.seqera.io/library/hisat2_samtools:9ef5e68250d2aa60' } }
19-
process { withName: 'HISAT2_BUILD' { container = 'community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } }
20-
process { withName: 'HISAT2_EXTRACTSPLICESITES' { container = 'community.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5' } }
21-
process { withName: 'KALLISTO_INDEX' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } }
22-
process { withName: 'KALLISTO_QUANT' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52' } }
23-
process { withName: 'KRAKEN2_KRAKEN2' { container = 'community.wave.seqera.io/library/kraken2_coreutils_pigz:0892e153c7954635' } }
24-
process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.27--b0d1ffb40dfd9e97' } }
25-
process { withName: 'MULTIQC_CUSTOM_BIOTYPE' { container = 'community.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a' } }
26-
process { withName: 'PICARD_MARKDUPLICATES' { container = 'community.wave.seqera.io/library/picard:3.1.1--bae6cd265e6bf3d3' } }
27-
process { withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = 'community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } }
28-
process { withName: 'PRESEQ_LCEXTRAP' { container = 'community.wave.seqera.io/library/preseq:3.2.0--2789d8b704b33613' } }
29-
process { withName: 'QUALIMAP_RNASEQ' { container = 'community.wave.seqera.io/library/qualimap:2.3--c1797c2253925b3a' } }
30-
process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } }
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process { withName: 'RSEM_MERGE_COUNTS' { container = 'community.wave.seqera.io/library/sed:4.7--c9d1b71422302845' } }
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process { withName: 'RSEM_PREPAREREFERENCE' { container = 'community.wave.seqera.io/library/rsem_star:5acb4e8c03239c32' } }
33-
process { withName: 'RSEQC_BAMSTAT' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
34-
process { withName: 'RSEQC_INFEREXPERIMENT' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
35-
process { withName: 'RSEQC_INNERDISTANCE' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
36-
process { withName: 'RSEQC_JUNCTIONANNOTATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
37-
process { withName: 'RSEQC_JUNCTIONSATURATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
38-
process { withName: 'RSEQC_READDISTRIBUTION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
39-
process { withName: 'RSEQC_READDUPLICATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
40-
process { withName: 'RSEQC_TIN' { container = 'community.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e' } }
41-
process { withName: 'SALMON_INDEX' { container = 'community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } }
42-
process { withName: 'SALMON_QUANT' { container = 'community.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423' } }
43-
process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } }
44-
process { withName: 'SAMTOOLS_IDXSTATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } }
45-
process { withName: 'SAMTOOLS_INDEX' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } }
46-
process { withName: 'SAMTOOLS_SORT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } }
47-
process { withName: 'SAMTOOLS_STATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf' } }
48-
process { withName: 'SORTMERNA' { container = 'community.wave.seqera.io/library/sortmerna:4.3.7--6502243397c065ba' } }
49-
process { withName: 'STAR_ALIGN' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } }
50-
process { withName: 'STAR_ALIGN_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } }
51-
process { withName: 'STAR_GENOMEGENERATE' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829' } }
52-
process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a' } }
53-
process { withName: 'STRINGTIE_STRINGTIE' { container = 'community.wave.seqera.io/library/stringtie:2.2.3--3c30041821e5a79a' } }
54-
process { withName: 'SUBREAD_FEATURECOUNTS' { container = 'community.wave.seqera.io/library/subread:2.0.6--1968a7457b0ed34e' } }
55-
process { withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = 'community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--13051b66560c2065' } }
56-
process { withName: 'TRIMGALORE' { container = 'community.wave.seqera.io/library/cutadapt_trim-galore_pigz:a98edd405b34582d' } }
57-
process { withName: 'TXIMETA_TXIMPORT' { container = 'community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--cd025af46d4ef23a' } }
58-
process { withName: 'UCSC_BEDCLIP' { container = 'community.wave.seqera.io/library/ucsc-bedclip:377--41de764ea1c26af4' } }
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process { withName: 'UCSC_BEDGRAPHTOBIGWIG' { container = 'community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--f66c00635e28f216' } }
60-
process { withName: 'UMICOLLAPSE' { container = 'community.wave.seqera.io/library/umicollapse:1.1.0--74864b350c72f3a0' } }
61-
process { withName: 'UMITOOLS_DEDUP' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } }
62-
process { withName: 'UMITOOLS_EXTRACT' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } }
63-
process { withName: 'UMITOOLS_PREPAREFORRSEM' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60' } }
64-
process { withName: 'UNTAR' { container = 'community.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc' } }
1+
process { withName: 'BBMAP_BBSPLIT' { container = 'community.wave.seqera.io/library/bbmap:39.10--908996c2fb304bec' } }
2+
process { withName: 'BEDTOOLS_GENOMECOV' { container = 'community.wave.seqera.io/library/bedtools:2.31.1--efd79503b8c63422' } }
3+
process { withName: 'BRACKEN_BRACKEN' { container = 'community.wave.seqera.io/library/bracken:2.9--e06b532ae215c74d' } }
4+
process { withName: 'CAT_FASTQ' { container = 'community.wave.seqera.io/library/coreutils:9.5--3931e2d27d9884e5' } }
5+
process { withName: 'CUSTOM_CATADDITIONALFASTA' { container = 'community.wave.seqera.io/library/python:3.12.2--0d47e6fe32e00784' } }
6+
process { withName: 'CUSTOM_GETCHROMSIZES' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } }
7+
process { withName: 'CUSTOM_TX2GENE' { container = 'community.wave.seqera.io/library/python:3.10.4--d0dc5eb8ea72fa82' } }
8+
process { withName: 'DESEQ2_QC' { container = 'community.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:8bd3e9db55b129d7' } }
9+
process { withName: 'DUPRADAR' { container = 'community.wave.seqera.io/library/bioconductor-dupradar:1.32.0--f75495d6abf45328' } }
10+
process { withName: 'FASTP' { container = 'community.wave.seqera.io/library/fastp:0.23.4--c1051f83dcae53f5' } }
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process { withName: 'FASTQC' { container = 'community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a' } }
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process { withName: 'FQ_LINT' { container = 'community.wave.seqera.io/library/fq:0.12.0--ad6857b304869ce9' } }
13+
process { withName: 'FQ_SUBSAMPLE' { container = 'community.wave.seqera.io/library/fq:0.12.0--ad6857b304869ce9' } }
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process { withName: 'GFFREAD' { container = 'community.wave.seqera.io/library/gffread:0.12.7--1577aa7c95340d9f' } }
15+
process { withName: 'GTF2BED' { container = 'community.wave.seqera.io/library/perl:5.26.2--2a6adf51d600e047' } }
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process { withName: 'GTF_FILTER' { container = 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } }
17+
process { withName: 'GUNZIP' { container = 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } }
18+
process { withName: 'HISAT2_ALIGN' { container = 'community.wave.seqera.io/library/hisat2_samtools:16f4ce5d5c83f6ec' } }
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process { withName: 'HISAT2_BUILD' { container = 'community.wave.seqera.io/library/hisat2:2.2.1--722945b3f185af3d' } }
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process { withName: 'HISAT2_EXTRACTSPLICESITES' { container = 'community.wave.seqera.io/library/hisat2:2.2.1--722945b3f185af3d' } }
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process { withName: 'KALLISTO_INDEX' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } }
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process { withName: 'KALLISTO_QUANT' { container = 'community.wave.seqera.io/library/kallisto:0.51.1--58dde61fc91c371b' } }
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process { withName: 'KRAKEN2_KRAKEN2' { container = 'community.wave.seqera.io/library/kraken2_coreutils_pigz:efede2ece83f7a32' } }
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process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.27--7cf5785022026d98' } }
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process { withName: 'MULTIQC_CUSTOM_BIOTYPE' { container = 'community.wave.seqera.io/library/python:3.9.5--d54415978b031ba5' } }
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process { withName: 'PICARD_MARKDUPLICATES' { container = 'community.wave.seqera.io/library/picard:3.1.1--c28da730a329ab3c' } }
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process { withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } }
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process { withName: 'PRESEQ_LCEXTRAP' { container = 'community.wave.seqera.io/library/preseq:3.2.0--80c9d2ffee38d3ac' } }
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process { withName: 'QUALIMAP_RNASEQ' { container = 'community.wave.seqera.io/library/qualimap:2.3--8375b60bba97a2a6' } }
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process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'community.wave.seqera.io/library/rsem_star:871666abaeb8fb01' } }
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process { withName: 'RSEM_MERGE_COUNTS' { container = 'community.wave.seqera.io/library/sed:4.7--978821297d2b6677' } }
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process { withName: 'RSEM_PREPAREREFERENCE' { container = 'community.wave.seqera.io/library/rsem_star:871666abaeb8fb01' } }
33+
process { withName: 'RSEQC_BAMSTAT' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
34+
process { withName: 'RSEQC_INFEREXPERIMENT' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
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process { withName: 'RSEQC_INNERDISTANCE' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
36+
process { withName: 'RSEQC_JUNCTIONANNOTATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
37+
process { withName: 'RSEQC_JUNCTIONSATURATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
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process { withName: 'RSEQC_READDISTRIBUTION' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
39+
process { withName: 'RSEQC_READDUPLICATION' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
40+
process { withName: 'RSEQC_TIN' { container = 'community.wave.seqera.io/library/rseqc_r-base:092fef07cff0abfa' } }
41+
process { withName: 'SALMON_INDEX' { container = 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } }
42+
process { withName: 'SALMON_QUANT' { container = 'community.wave.seqera.io/library/salmon:1.10.3--dc33937abc5bffd1' } }
43+
process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } }
44+
process { withName: 'SAMTOOLS_IDXSTATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } }
45+
process { withName: 'SAMTOOLS_INDEX' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } }
46+
process { withName: 'SAMTOOLS_SORT' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } }
47+
process { withName: 'SAMTOOLS_STATS' { container = 'community.wave.seqera.io/library/htslib_samtools:1.21--1dcf014b5ab22a61' } }
48+
process { withName: 'SORTMERNA' { container = 'community.wave.seqera.io/library/sortmerna:4.3.7--4cc83a7bffbaaa61' } }
49+
process { withName: 'STAR_ALIGN' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:de8c848656c2c4c5' } }
50+
process { withName: 'STAR_ALIGN_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:6ae64d775f2cb855' } }
51+
process { withName: 'STAR_GENOMEGENERATE' { container = 'community.wave.seqera.io/library/htslib_samtools_star_gawk:de8c848656c2c4c5' } }
52+
process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'community.wave.seqera.io/library/star_samtools_gawk:6ae64d775f2cb855' } }
53+
process { withName: 'STRINGTIE_STRINGTIE' { container = 'community.wave.seqera.io/library/stringtie:2.2.3--77d8df3265c94ba1' } }
54+
process { withName: 'SUBREAD_FEATURECOUNTS' { container = 'community.wave.seqera.io/library/subread:2.0.6--df9c6b502b57bb9c' } }
55+
process { withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = 'community.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--859858039875a2a5' } }
56+
process { withName: 'TRIMGALORE' { container = 'community.wave.seqera.io/library/cutadapt_trim-galore_pigz:d0b730b6770575ef' } }
57+
process { withName: 'TXIMETA_TXIMPORT' { container = 'community.wave.seqera.io/library/bioconductor-tximeta:1.20.1--3b0ca8a1710e2b2b' } }
58+
process { withName: 'UCSC_BEDCLIP' { container = 'community.wave.seqera.io/library/ucsc-bedclip:377--489576e83f1992e0' } }
59+
process { withName: 'UCSC_BEDGRAPHTOBIGWIG' { container = 'community.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--1db18e1b19f8e5f1' } }
60+
process { withName: 'UMICOLLAPSE' { container = 'community.wave.seqera.io/library/umicollapse:1.1.0--d406900dbf84ec60' } }
61+
process { withName: 'UMITOOLS_DEDUP' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } }
62+
process { withName: 'UMITOOLS_EXTRACT' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } }
63+
process { withName: 'UMITOOLS_PREPAREFORRSEM' { container = 'community.wave.seqera.io/library/umi_tools:1.1.5--b2721816f7a92564' } }
64+
process { withName: 'UNTAR' { container = 'community.wave.seqera.io/library/grep_sed_tar:4b2523b1c76a5494' } }

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