diff --git a/genome-alignment-star/Dockerfile b/genome-alignment-star/Dockerfile index 8b1b221..eba2325 100644 --- a/genome-alignment-star/Dockerfile +++ b/genome-alignment-star/Dockerfile @@ -1,8 +1,8 @@ FROM ratschlab/wf-base-miniconda4.8.3:v1.0.1 -LABEL org.opencontainers.image.source https://github.com/icgc-argo-rna-wg/icgc-argo-rna-seq-alignment +LABEL org.opencontainers.image.source https://github.com/ratschlab/wftools-alignment-rna LABEL org.opencontainers.image.authors Andre Kahles (andre.kahles@inf.ethz.ch) -LABEL org.opencontainers.image.title ICGC ARGO RNA-Seq alignment image +LABEL org.opencontainers.image.title Raetschlab RNA-Seq alignment image - STAR ENV PATH="/opt/local:${PATH}" diff --git a/genome-alignment-star/main.nf b/genome-alignment-star/main.nf index e4040c3..d5bef74 100755 --- a/genome-alignment-star/main.nf +++ b/genome-alignment-star/main.nf @@ -1,7 +1,7 @@ #!/usr/bin/env nextflow /* - Copyright (c) 2021, icgc-argo-rna-wg + Copyright (c) 2021, ratschlab Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal @@ -57,7 +57,7 @@ params.sample = "" params.sjdboverhang = 100 params.pair_status = "paired" -process icgcArgoRnaSeqAlignmentSTAR { +process genomeAlignmentSTAR { container "${params.container ?: container[params.container_registry ?: default_container_registry]}:${params.container_version ?: version}" publishDir "${params.publish_dir}/${task.process.replaceAll(':', '_')}", mode: "copy", enabled: params.publish_dir @@ -96,7 +96,7 @@ process icgcArgoRnaSeqAlignmentSTAR { // this provides an entry point for this main script, so it can be run directly without clone the repo // using this command: nextflow run ///.nf -r .v --params-file xxx workflow { - icgcArgoRnaSeqAlignmentSTAR( + genomeAlignmentSTAR( file(params.index), file(params.gtf), params.input_files.collect({it -> file(it)}), diff --git a/genome-alignment-star/tests/checker.nf b/genome-alignment-star/tests/checker.nf index 3872fbb..22dd377 100755 --- a/genome-alignment-star/tests/checker.nf +++ b/genome-alignment-star/tests/checker.nf @@ -1,7 +1,7 @@ #!/usr/bin/env nextflow /* - Copyright (c) 2021, icgc-argo-rna-wg + Copyright (c) 2021, ratschlab Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal @@ -56,7 +56,7 @@ params.sjdboverhang = 100 params.pair_status = "paired" params.expected_output = "tests/expected/sample_01_Aligned.out.bam" -include { icgcArgoRnaSeqAlignmentSTAR } from '../main' params(['cleanup': false, *:params]) +include { genomeAlignmentSTAR } from '../main' params(['cleanup': false, *:params]) process diff_bam { container "${params.container ?: container[params.container_registry ?: default_container_registry]}:${params.container_version ?: version}" @@ -106,7 +106,7 @@ workflow checker { expected_junctions main: - icgcArgoRnaSeqAlignmentSTAR( + genomeAlignmentSTAR( index, gtf, input_files, @@ -117,12 +117,12 @@ workflow checker { ) diff_bam( - icgcArgoRnaSeqAlignmentSTAR.out.bam, + genomeAlignmentSTAR.out.bam, expected_bam ) diff_junctions( - icgcArgoRnaSeqAlignmentSTAR.out.junctions, + genomeAlignmentSTAR.out.junctions, expected_junctions ) }