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nf-core_modules/modules/ascat/meta.yml

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ASCAT (#1332) * First commit * putting correct links for singularity and docker containers (just had to search for bioconda+ascat to find them, and then put them in like the rest of the nf-core tools had it * adding first try of relevant commands (not working yet, just took their basic pipeline example * test commit * remove test * starting up work with module after 3.0.0 upgrade * add ascat.prepareHTS statemet * add location of docker for new mulled alleleCounter+ASCAT container * first full run with ASCAT on HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam * add notes on dropbox download * use a newer pytest_modules.yml * add outpit * trying to align with current Sarek output * adding in FH comments * busy clearing up arguments and testing. Still WIP * first working run, in nextflow, with sarek-like output. Still needs more work on input arguments * cleaning up before writing up findings * testing with putting in arguments in args * draft for solution 3 style for arguments * one more test added * adding FH map * finished testing maps for args * wrap-up cram/crai test successfully * updates to address ability to put in ref.fasta argument for cram running * adding remaining import-HTS commands in as args, and removing the chr21/chr22 only testing to test-nextflow.config * first test with auto-downloading the s3-data (when not given as an argument) * removing download-logic for supporting files, documenting in meta.yml, fixing ref_fasta bug * adding mulled singularity container * removing tests * fix left padding lint issue * lint failure in meta.yml * more linting errors * add when argument * adding stub functionality * add stub run * correct md5sum for versions.yml * more testing with -runstub * stub code in pure bash - not mixed with R * reformat version.yml * get rid of absolute paths in test.yml * correct wrong md5sum * adding allelecount conda link * rename normal_bam to input_bam etc * let the pipeline dev worry about matching the right loci and allele files * dont hardcode default genomebuild * adding download instruction comment * add doi * fix conda addition bug * add args documentation * test new indent * new test with meta.yml indentation * retry with new meta.yml * retry with new meta.yml - now with empty lines around * retry with new meta.yml - remove trailing whitepsace * trying to fix found quote character that cannot start any token error * try with one empty line above triple-quote and no empty line below * trying with pipe character * checking if its the ending triple quote * one more try with meta.yml * test update bioconda versioning for linting failure * test update bioconda versioning for linting failure 2 * testing allelecounter version error on conda Co-authored-by: @lassefolkersen Co-authored-by: @FriederikeHanssen
2022-03-15 10:18:43 +00:00
name: ascat
description: copy number profiles of tumour cells.
keywords:
- sort
tools:
- ascat:
description: ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy. ASCAT infers tumour purity (the fraction of tumour cells) and ploidy (the amount of DNA per tumour cell), expressed as multiples of haploid genomes from SNP array or massively parallel sequencing data, and calculates whole-genome allele-specific copy number profiles (the number of copies of both parental alleles for all SNP loci across the genome).
homepage: None
documentation: None
tool_dev_url: https://github.com/Crick-CancerGenomics/ascat
doi: "10.1093/bioinformatics/btaa538"
Prettier (#1405) * style: Add prettier config files * build: Add prettier vscode extension * ci: Replace markdownlint and yamllint with prettier * style: Run prettier * style: Use indent of 2 for markdown as well https://github.com/nf-core/tools/pull/1470#issuecomment-1071028358 * style: Fix indent * style: Let editorconfig take over tab widths * style: yaml => yml * ci: Run prettier once Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se> Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
2022-03-18 13:27:50 +00:00
licence: ["GPL v3"]
ASCAT (#1332) * First commit * putting correct links for singularity and docker containers (just had to search for bioconda+ascat to find them, and then put them in like the rest of the nf-core tools had it * adding first try of relevant commands (not working yet, just took their basic pipeline example * test commit * remove test * starting up work with module after 3.0.0 upgrade * add ascat.prepareHTS statemet * add location of docker for new mulled alleleCounter+ASCAT container * first full run with ASCAT on HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam * add notes on dropbox download * use a newer pytest_modules.yml * add outpit * trying to align with current Sarek output * adding in FH comments * busy clearing up arguments and testing. Still WIP * first working run, in nextflow, with sarek-like output. Still needs more work on input arguments * cleaning up before writing up findings * testing with putting in arguments in args * draft for solution 3 style for arguments * one more test added * adding FH map * finished testing maps for args * wrap-up cram/crai test successfully * updates to address ability to put in ref.fasta argument for cram running * adding remaining import-HTS commands in as args, and removing the chr21/chr22 only testing to test-nextflow.config * first test with auto-downloading the s3-data (when not given as an argument) * removing download-logic for supporting files, documenting in meta.yml, fixing ref_fasta bug * adding mulled singularity container * removing tests * fix left padding lint issue * lint failure in meta.yml * more linting errors * add when argument * adding stub functionality * add stub run * correct md5sum for versions.yml * more testing with -runstub * stub code in pure bash - not mixed with R * reformat version.yml * get rid of absolute paths in test.yml * correct wrong md5sum * adding allelecount conda link * rename normal_bam to input_bam etc * let the pipeline dev worry about matching the right loci and allele files * dont hardcode default genomebuild * adding download instruction comment * add doi * fix conda addition bug * add args documentation * test new indent * new test with meta.yml indentation * retry with new meta.yml * retry with new meta.yml - now with empty lines around * retry with new meta.yml - remove trailing whitepsace * trying to fix found quote character that cannot start any token error * try with one empty line above triple-quote and no empty line below * trying with pipe character * checking if its the ending triple quote * one more try with meta.yml * test update bioconda versioning for linting failure * test update bioconda versioning for linting failure 2 * testing allelecounter version error on conda Co-authored-by: @lassefolkersen Co-authored-by: @FriederikeHanssen
2022-03-15 10:18:43 +00:00
input:
- args:
type: map
description: |
round the < to ( to make markdown work for meta.yml (#1395) * round the < to ( to make markdown work for meta.yml * changing md5sums and stub output so it doesnt trigger the empty file linting error
2022-03-16 12:29:11 +00:00
Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes. (optional) parameters can be removed from the map, if they are not set. For default values, please check the documentation above.
ASCAT (#1332) * First commit * putting correct links for singularity and docker containers (just had to search for bioconda+ascat to find them, and then put them in like the rest of the nf-core tools had it * adding first try of relevant commands (not working yet, just took their basic pipeline example * test commit * remove test * starting up work with module after 3.0.0 upgrade * add ascat.prepareHTS statemet * add location of docker for new mulled alleleCounter+ASCAT container * first full run with ASCAT on HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam * add notes on dropbox download * use a newer pytest_modules.yml * add outpit * trying to align with current Sarek output * adding in FH comments * busy clearing up arguments and testing. Still WIP * first working run, in nextflow, with sarek-like output. Still needs more work on input arguments * cleaning up before writing up findings * testing with putting in arguments in args * draft for solution 3 style for arguments * one more test added * adding FH map * finished testing maps for args * wrap-up cram/crai test successfully * updates to address ability to put in ref.fasta argument for cram running * adding remaining import-HTS commands in as args, and removing the chr21/chr22 only testing to test-nextflow.config * first test with auto-downloading the s3-data (when not given as an argument) * removing download-logic for supporting files, documenting in meta.yml, fixing ref_fasta bug * adding mulled singularity container * removing tests * fix left padding lint issue * lint failure in meta.yml * more linting errors * add when argument * adding stub functionality * add stub run * correct md5sum for versions.yml * more testing with -runstub * stub code in pure bash - not mixed with R * reformat version.yml * get rid of absolute paths in test.yml * correct wrong md5sum * adding allelecount conda link * rename normal_bam to input_bam etc * let the pipeline dev worry about matching the right loci and allele files * dont hardcode default genomebuild * adding download instruction comment * add doi * fix conda addition bug * add args documentation * test new indent * new test with meta.yml indentation * retry with new meta.yml * retry with new meta.yml - now with empty lines around * retry with new meta.yml - remove trailing whitepsace * trying to fix found quote character that cannot start any token error * try with one empty line above triple-quote and no empty line below * trying with pipe character * checking if its the ending triple quote * one more try with meta.yml * test update bioconda versioning for linting failure * test update bioconda versioning for linting failure 2 * testing allelecounter version error on conda Co-authored-by: @lassefolkersen Co-authored-by: @FriederikeHanssen
2022-03-15 10:18:43 +00:00
```
{
[
"gender": "XX",
"genomeVersion": "hg19"
round the < to ( to make markdown work for meta.yml (#1395) * round the < to ( to make markdown work for meta.yml * changing md5sums and stub output so it doesnt trigger the empty file linting error
2022-03-16 12:29:11 +00:00
"purity": (optional),
"ploidy": (optional),
"gc_files": (optional),
"minCounts": (optional),
"chrom_names": (optional),
"min_base_qual": (optional),
"min_map_qual": (optional),
"ref_fasta": (optional),
"skip_allele_counting_tumour": (optional),
"skip_allele_counting_normal": (optional)
ASCAT (#1332) * First commit * putting correct links for singularity and docker containers (just had to search for bioconda+ascat to find them, and then put them in like the rest of the nf-core tools had it * adding first try of relevant commands (not working yet, just took their basic pipeline example * test commit * remove test * starting up work with module after 3.0.0 upgrade * add ascat.prepareHTS statemet * add location of docker for new mulled alleleCounter+ASCAT container * first full run with ASCAT on HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam * add notes on dropbox download * use a newer pytest_modules.yml * add outpit * trying to align with current Sarek output * adding in FH comments * busy clearing up arguments and testing. Still WIP * first working run, in nextflow, with sarek-like output. Still needs more work on input arguments * cleaning up before writing up findings * testing with putting in arguments in args * draft for solution 3 style for arguments * one more test added * adding FH map * finished testing maps for args * wrap-up cram/crai test successfully * updates to address ability to put in ref.fasta argument for cram running * adding remaining import-HTS commands in as args, and removing the chr21/chr22 only testing to test-nextflow.config * first test with auto-downloading the s3-data (when not given as an argument) * removing download-logic for supporting files, documenting in meta.yml, fixing ref_fasta bug * adding mulled singularity container * removing tests * fix left padding lint issue * lint failure in meta.yml * more linting errors * add when argument * adding stub functionality * add stub run * correct md5sum for versions.yml * more testing with -runstub * stub code in pure bash - not mixed with R * reformat version.yml * get rid of absolute paths in test.yml * correct wrong md5sum * adding allelecount conda link * rename normal_bam to input_bam etc * let the pipeline dev worry about matching the right loci and allele files * dont hardcode default genomebuild * adding download instruction comment * add doi * fix conda addition bug * add args documentation * test new indent * new test with meta.yml indentation * retry with new meta.yml * retry with new meta.yml - now with empty lines around * retry with new meta.yml - remove trailing whitepsace * trying to fix found quote character that cannot start any token error * try with one empty line above triple-quote and no empty line below * trying with pipe character * checking if its the ending triple quote * one more try with meta.yml * test update bioconda versioning for linting failure * test update bioconda versioning for linting failure 2 * testing allelecounter version error on conda Co-authored-by: @lassefolkersen Co-authored-by: @FriederikeHanssen
2022-03-15 10:18:43 +00:00
]
}
```
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input_normal:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- index_normal:
type: file
description: index for normal_bam
pattern: "*.{bai}"
- input_tumor:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- index_tumor:
type: file
description: index for tumor_bam
pattern: "*.{bai}"
- allele_files:
type: file
description: allele files for ASCAT. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS
- loci_files:
type: file
description: loci files for ASCAT. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- png:
type: file
description: ASCAT plots
pattern: "*.{png}"
- purityploidy:
type: file
description: purity and ploidy data
pattern: "*.purityploidy.txt"
- segments:
type: file
description: segments data
pattern: "*.segments.txt"
authors:
- "@aasNGC"
- "@lassefolkersen"
- "@FriederikeHanssen"
- "@maxulysse"
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