diff --git a/software/samtools/sort/meta.yml b/software/samtools/sort/meta.yml new file mode 100644 index 00000000..1e042f0d --- /dev/null +++ b/software/samtools/sort/meta.yml @@ -0,0 +1,27 @@ +name: samtools sort +description: Sort a BAM or CRAM file +keywords: + - sort +tools: + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 +input: + - + - input: + type: file + description: Input BAM or CRAM file + pattern: "*.{bam,cram}" +output: + - + - sorted_file: + type: file + description: Sorted BAM or CRAM file + pattern: "*.{bam,cram}" +authors: + - "@ewels" diff --git a/software/samtools/sort/test/main.nf b/software/samtools/sort/test/main.nf new file mode 100644 index 00000000..5fb89109 --- /dev/null +++ b/software/samtools/sort/test/main.nf @@ -0,0 +1,13 @@ +#!/usr/bin/env nextflow +echo true + +cheers = Channel.from 'Bonjour', 'Ciao', 'Hello', 'Hola' + +process sayHello { + input: + val x from cheers + script: + """ + echo '$x world!' + """ +} diff --git a/software/samtools/sort/test/nextflow.config b/software/samtools/sort/test/nextflow.config new file mode 100644 index 00000000..c137a138 --- /dev/null +++ b/software/samtools/sort/test/nextflow.config @@ -0,0 +1,2 @@ +docker.enabled = true +params.outdir = './results'