nf-core_modules/tests/modules/ascat/main.nf
Lasse Folkersen d6244b42f5
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 11:18:43 +01:00

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3.6 KiB
Text

#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { ASCAT as ASCAT_SIMPLE} from '../../../modules/ascat/main.nf'
include { ASCAT as ASCAT_PLOIDY_AND_PURITY} from '../../../modules/ascat/main.nf'
include { ASCAT as ASCAT_CRAM} from '../../../modules/ascat/main.nf'
workflow test_ascat {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)
]
ASCAT_SIMPLE ( input , [], [])
}
// extended tests running with 1000 genomes data. Data is downloaded as follows:
// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00154/alignment/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai
// wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00155/alignment/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam
// wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/data/HG00155/alignment/HG00155.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai
//workflow test_ascat_with_ploidy_and_purity {
// input = [
// [ id:'test', single_end:false ], // meta map
// file("/home/ec2-user/input_files/bams/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam", checkIfExists: true),
// file("/home/ec2-user/input_files/bams/HG00154.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123.bam.bai", checkIfExists: true),
// file("/home/ec2-user/input_files/bams/test2.bam", checkIfExists: true),
// file("/home/ec2-user/input_files/bams/test2.bam.bai", checkIfExists: true)
// ]
//
// ASCAT_PLOIDY_AND_PURITY ( input , "/home/ec2-user/input_files/allele_files/G1000_alleles_hg19_chr", "/home/ec2-user/input_files/loci_files/G1000_alleles_hg19_chr")
//}
// extended tests running with 1000 genomes data. Data is downloaded as follows:
// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00145/alignment/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai
// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00145/alignment/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram
// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00146/alignment/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai
// wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00146/alignment/HG00146.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram
//workflow test_ascat_with_crams {
// input = [
// [ id:'test', single_end:false ], // meta map
// file("/home/ec2-user/input_files/crams/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram", checkIfExists: true),
// file("/home/ec2-user/input_files/crams/HG00145.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam.cram.crai", checkIfExists: true),
// file("/home/ec2-user/input_files/crams/duplicate_test.cram", checkIfExists: true),
// file("/home/ec2-user/input_files/crams/duplicate_test.cram.crai", checkIfExists: true)
// ]
//
// ASCAT_CRAM ( input , "/home/ec2-user/input_files/allele_files/G1000_alleles_hg19_chr", "/home/ec2-user/input_files/loci_files/G1000_alleles_hg19_chr")
//}