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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,94 @@ | ||
| name: samtools_collate | ||
| namespace: samtools | ||
| description: Shuffles and groups reads in SAM/BAM/CRAM files together by their names. | ||
| keywords: [collate, counts, bam, sam, cram] | ||
| links: | ||
| homepage: https://www.htslib.org/ | ||
| documentation: https://www.htslib.org/doc/samtools-icollate.html | ||
| repository: https://github.com/samtools/samtools | ||
| references: | ||
| doi: [10.1093/bioinformatics/btp352, 10.1093/gigascience/giab008] | ||
| license: MIT/Expat | ||
|
|
||
| argument_groups: | ||
| - name: Inputs | ||
| arguments: | ||
| - name: --input | ||
| type: file | ||
| description: The input BAM file. | ||
| required: true | ||
| - name: --reference | ||
| type: file | ||
| description: Reference sequence FASTA FILE. | ||
|
|
||
| - name: Outputs | ||
| arguments: | ||
| - name: --output | ||
| alternatives: -o | ||
| type: file | ||
| description: The output filename. | ||
| required: true | ||
| direction: output | ||
|
|
||
| - name: Options | ||
| arguments: | ||
| - name: --uncompressed | ||
| alternatives: -u | ||
| type: boolean_true | ||
| description: Output uncompressed BAM. | ||
| - name: --fast | ||
| alternatives: -f | ||
| type: boolean_true | ||
| description: Fast mode, only primary alignments. | ||
| - name: --working_reads | ||
| alternatives: -r | ||
| type: integer | ||
| description: Working reads stored (for use with -f). | ||
| default: 10000 | ||
| - name: --compression | ||
| alternatives: -l | ||
| type: integer | ||
| description: Compression level. | ||
| default: 1 | ||
| - name: --nb_tmp_files | ||
| alternatives: -n | ||
| type: integer | ||
| description: Number of temporary files. | ||
| default: 64 | ||
| - name: --tmp_prefix | ||
| alternatives: -T | ||
| type: string | ||
| description: Write temporary files to PREFIX.nnnn.bam. | ||
| - name: --no_pg | ||
| type: boolean_true | ||
| description: Do not add a PG line. | ||
| - name: --input_fmt_option | ||
| type: string | ||
| description: Specify a single input file format option in the form of OPTION or OPTION=VALUE. | ||
| - name: --output_fmt | ||
| type: string | ||
| description: Specify output format (SAM, BAM, CRAM). | ||
| - name: --output_fmt_option | ||
| type: string | ||
| description: Specify a single output file format option in the form of OPTION or OPTION=VALUE. | ||
|
|
||
|
|
||
| resources: | ||
| - type: bash_script | ||
| path: script.sh | ||
| test_resources: | ||
| - type: bash_script | ||
| path: test.sh | ||
| - type: file | ||
| path: test_data | ||
| engines: | ||
| - type: docker | ||
| image: quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1 | ||
| setup: | ||
| - type: docker | ||
| run: | | ||
| samtools --version 2>&1 | grep -E '^(samtools|Using htslib)' | \ | ||
| sed 's#Using ##;s# \([0-9\.]*\)$#: \1#' > /var/software_versions.txt | ||
| runners: | ||
| - type: executable | ||
| - type: nextflow |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| ``` | ||
| samtools collate | ||
| ``` | ||
| Usage: samtools collate [options...] <in.bam> [<prefix>] | ||
|
|
||
| Options: | ||
| -O Output to stdout | ||
| -o Output file name (use prefix if not set) | ||
| -u Uncompressed BAM output | ||
| -f Fast (only primary alignments) | ||
| -r Working reads stored (with -f) [10000] | ||
| -l INT Compression level [1] | ||
| -n INT Number of temporary files [64] | ||
| -T PREFIX | ||
| Write temporary files to PREFIX.nnnn.bam | ||
| --no-PG do not add a PG line | ||
| --input-fmt-option OPT[=VAL] | ||
| Specify a single input file format option in the form | ||
| of OPTION or OPTION=VALUE | ||
| --output-fmt FORMAT[,OPT[=VAL]]... | ||
| Specify output format (SAM, BAM, CRAM) | ||
| --output-fmt-option OPT[=VAL] | ||
| Specify a single output file format option in the form | ||
| of OPTION or OPTION=VALUE | ||
| --reference FILE | ||
| Reference sequence FASTA FILE [null] | ||
| -@, --threads INT | ||
| Number of additional threads to use [0] | ||
| --verbosity INT | ||
| Set level of verbosity | ||
| <prefix> is required unless the -o or -O options are used. |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,27 @@ | ||
| #!/bin/bash | ||
|
|
||
| ## VIASH START | ||
| ## VIASH END | ||
|
|
||
| set -e | ||
|
|
||
| [[ "$par_uncompressed" == "false" ]] && unset par_uncompressed | ||
| [[ "$par_fast" == "false" ]] && unset par_fast | ||
| [[ "$par_no_pg" == "false" ]] && unset par_no_pg | ||
|
|
||
| samtools collate \ | ||
| "$par_input" \ | ||
| ${par_output:+-o "$par_output"} \ | ||
| ${par_reference:+-T "$par_reference"} \ | ||
| ${par_uncompressed:+-u} \ | ||
| ${par_fast:+-f} \ | ||
| ${par_working_reads:+-r "$par_working_reads"} \ | ||
| ${par_compression:+-l "$par_compression"} \ | ||
| ${par_nb_tmp_files:+-n "$par_nb_tmp_files"} \ | ||
| ${par_tmp_prefix:+-T "$par_tmp_prefix"} \ | ||
| ${par_no_pg:+-P} \ | ||
| ${par_input_fmt_option:+-O "$par_input_fmt_option"} \ | ||
| ${par_output_fmt:+-O "$par_output_fmt"} \ | ||
| ${par_output_fmt_option:+-O "$par_output_fmt_option"} | ||
|
|
||
| exit 0 |
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