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| author | Arun Isaac | 2021-03-17 23:58:08 +0530 |
|---|---|---|
| committer | Arun Isaac | 2021-03-17 23:58:08 +0530 |
| commit | 82336f79f04ccf37849f7ef1814f60fb85f3a738 (patch) | |
| tree | e2424c201f46de84dac2027cbf09be8c73dd23c4 /scripts/variant-calling-bowtie-bwa-mem.scm | |
| parent | f8a9462c56b481d34af5d142fb746974c7d7bc5c (diff) | |
| download | bh20-seq-resource-82336f79f04ccf37849f7ef1814f60fb85f3a738.tar.gz bh20-seq-resource-82336f79f04ccf37849f7ef1814f60fb85f3a738.tar.lz bh20-seq-resource-82336f79f04ccf37849f7ef1814f60fb85f3a738.zip | |
Use default output of pipeline generate-cwl
Diffstat (limited to 'scripts/variant-calling-bowtie-bwa-mem.scm')
| -rw-r--r-- | scripts/variant-calling-bowtie-bwa-mem.scm | 21 |
1 files changed, 8 insertions, 13 deletions
diff --git a/scripts/variant-calling-bowtie-bwa-mem.scm b/scripts/variant-calling-bowtie-bwa-mem.scm index 88498f6..5ddc1f6 100644 --- a/scripts/variant-calling-bowtie-bwa-mem.scm +++ b/scripts/variant-calling-bowtie-bwa-mem.scm @@ -35,17 +35,14 @@ (list "samtools" "sort" "-")) (command "samtools_markdup" (list "samtools" "markdup" "-" "-") - #:other '((stdout . "dedup.bam")))) - (list (output "dedup_bam" - #:source "samtools_markdup/stdout"))) + #:other '((stdout . "dedup.bam"))))) (command "samtools_index" - (list "samtools" "index" - (input "dedup_bam")) + (list "samtools" "index" (input "samtools_stdout")) #:outputs (list (output "indexed_dedup_bam" - #:binding '((glob . "$(inputs.dedup_bam.basename)")) + #:binding '((glob . "$(inputs.samtools_stdout.basename)")) #:other '((secondary-files . #(".bai"))))) #:other `((hints (Initial-work-dir-requirement - (listing . #("$(inputs.dedup_bam)")))))) + (listing . #("$(inputs.samtools_stdout)")))))) (pipeline "freebayes" (list (command "freebayes" (list "freebayes" "--ploidy" "1" @@ -56,16 +53,14 @@ (list "bcftools" "view" "-i" "QUAL > 10" "-Oz") - #:other `((stdout . ,(string-append prefix "_output.vcf.gz"))))) - (list (output "vcf" - #:source "bcftools_view/stdout"))) + #:other `((stdout . ,(string-append prefix "_output.vcf.gz")))))) (command "tabix" - (list "tabix" (input "vcf")) + (list "tabix" (input "freebayes_stdout")) #:outputs (list (output "indexed_vcf" - #:binding '((glob . "$(inputs.vcf.basename)")) + #:binding '((glob . "$(inputs.freebayes_stdout.basename)")) #:other '((secondary-files . #(".tbi"))))) #:other `((hints (Initial-work-dir-requirement - (listing . #("$(inputs.vcf)"))))))) + (listing . #("$(inputs.freebayes_stdout)"))))))) (list (output (string-append prefix "_output") #:source "tabix/indexed_vcf")))) |