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update how PipeVal is being used to validate input and output files #240
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@@ -14,12 +14,13 @@ params { | |
// tools and their versions | ||
bwa_version = "BWA-MEM2-2.2.1" | ||
hisat2_version = "HISAT2-2.2.1" | ||
pipeval_version = "2.1.6" | ||
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docker_image_bwa_and_samtools = "blcdsdockerregistry/bwa-mem2_samtools-1.12:2.2.1" | ||
docker_image_hisat2_and_samtools = "blcdsdockerregistry/hisat2_samtools-1.12:2.2.1" | ||
docker_image_picardtools = "blcdsdockerregistry/picard:2.26.10" | ||
docker_image_sha512sum = "blcdsdockerregistry/align-dna:sha512sum-1.0" | ||
docker_image_validate_params = "blcdsdockerregistry/validate:2.1.5" | ||
docker_image_validate_params = "blcdsdockerregistry/validate:2.1.6" | ||
docker_image_gatk = "broadinstitute/gatk:4.2.4.1" | ||
docker_image_samtools = "blcdsdockerregistry/samtools:1.15.1" | ||
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// samtools due to the large size of the uncompressed SAM files. | ||
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include { run_sort_SAMtools ; run_merge_SAMtools} from './samtools.nf' | ||
include { run_validate_PipeVal; run_validate_PipeVal as validate_output_file } from './validation.nf' | ||
include { run_validate_PipeVal; run_validate_PipeVal as validate_output_file } from '../external/nextflow-modules/modules/PipeVal/validate/main.nf' | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Does the workflow for HISAT2 not require updates like the ones with BWA-MEM2? There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. The HISAT2 workflow needs to get the same updates. However, I cannot get PipeVal to work in the BWA-MEM2 workflow (see previous comments), so I am waiting to update HISAT2. I don't understand what PipeVal is doing on the current
BWA-MEM2:
HISAT2:
Nearly all files are There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Most of the files are Align-DNA also tries to validate the We may need to wait for pipeval to get updated before we can proceed with this PR. |
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include { run_MarkDuplicate_Picard } from './mark_duplicate_picardtools.nf' | ||
include { run_MarkDuplicatesSpark_GATK } from './mark_duplicates_spark.nf' | ||
include { generate_sha512sum } from './check_512sum.nf' | ||
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We might want to specify that we're using
v3.0.0
; the module might get updated to newer versions but the version used by the pipeline is still dictated by indefault.config