@@ -12,24 +12,30 @@ docker.registry = 'public.ecr.aws'
1212podman.registry = 'public.ecr.aws'
1313
1414process {
15+ withName: 'CAT_ADDITIONAL_FASTA' {
16+ container = 'quay.io/biocontainers/python:3.9--1'
17+ }
1518 withName: 'CAT_FASTQ' {
1619 container = 'quay.io/nf-core/ubuntu:20.04'
1720 }
18- withName: 'SAMPLESHEET_CHECK|CAT_ADDITIONAL_FASTA|GTF_GENE_FILTER|MULTIQC_CUSTOM_BIOTYPE|SALMON_TX2GENE ' {
19- container = 'quay.io/biocontainers/python:3.9--1 '
21+ withName: 'DESEQ2_QC ' {
22+ container = 'quay.io/biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0 '
2023 }
2124 withName: 'GTF2BED' {
2225 container = 'quay.io/biocontainers/perl:5.26.2'
2326 }
24- withName: 'DESEQ2_QC ' {
25- container = 'quay.io/biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0 '
27+ withName: 'GTF_GENE_FILTER ' {
28+ container = 'quay.io/biocontainers/python:3.9--1 '
2629 }
2730 withName: 'GUNZIP' {
2831 container = 'quay.io/nf-core/ubuntu:20.04'
2932 }
3033 withName: 'HISAT2_ALIGN' {
3134 container = 'quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0'
3235 }
36+ withName: 'MULTIQC_CUSTOM_BIOTYPE' {
37+ container = 'quay.io/biocontainers/python:3.9--1'
38+ }
3339 withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' {
3440 container = 'quay.io/nf-core/ubuntu:20.04'
3541 }
@@ -42,6 +48,12 @@ process {
4248 withName: 'RSEM_PREPAREREFERENCE' {
4349 container = 'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0'
4450 }
51+ withName: 'SALMON_TX2GENE' {
52+ container = 'quay.io/biocontainers/python:3.9--1'
53+ }
54+ withName: 'SAMPLESHEET_CHECK' {
55+ container = 'quay.io/biocontainers/python:3.9--1'
56+ }
4557 withName: 'STAR_ALIGN' {
4658 container = 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0'
4759 }
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