diff options
| -rw-r--r-- | scripts/fastq2fasta.scm | 18 | ||||
| -rw-r--r-- | scripts/variant-calling-bowtie-bwa-mem.scm | 21 |
2 files changed, 15 insertions, 24 deletions
diff --git a/scripts/fastq2fasta.scm b/scripts/fastq2fasta.scm index 590a535..ddb507d 100644 --- a/scripts/fastq2fasta.scm +++ b/scripts/fastq2fasta.scm @@ -34,7 +34,7 @@ (define fastq2fasta (workflow "fastq2fasta" - (list (pipeline "bwa_mem_to_normalized" + (list (pipeline "normalization" (list (command "bwa_mem" (list "bwa" "mem" "-t" threads ref-fasta fastq-forward fastq-reverse)) @@ -51,16 +51,14 @@ (command "bcftools_norm" (list "bcftools" "norm" "-Ob" "-f" ref-fasta "--threads" threads "-") - #:other '((stdout . "normalized.bcf")))) - (list (output "normalized" - #:source "bcftools_norm/stdout"))) + #:other '((stdout . "normalized.bcf"))))) (command "bcftools_index_after_normalization" - (list "bcftools" "index" (input "normalized")) + (list "bcftools" "index" (input "normalization_stdout")) #:outputs (list (output "index_after_normalization" - #:binding '((glob . "$(inputs.normalized.basename)")) + #:binding '((glob . "$(inputs.normalization_stdout.basename)")) #:other '((secondary-files . #(".csi"))))) #:other `((hints (Initial-work-dir-requirement - (listing . #("$(inputs.normalized)")))))) + (listing . #("$(inputs.normalization_stdout)")))))) (command "bcftools_view_qc" (list "bcftools" "view" "-i" "'QUAL > 10 && GT=\"a\"'" @@ -85,10 +83,8 @@ #:other '((secondary-files . #(".csi")))))) (command "set_sample_id" (list "sed" "s/^>.*/>$(inputs.sample_id)/g") - #:additional-inputs (list sample-id))) - (list (output "out_fasta" - #:source "set_sample_id/stdout")))) + #:additional-inputs (list sample-id))))) (list (output "out_fasta" - #:source "consensus/out_fasta")))) + #:source "consensus/consensus_stdout")))) (write-cwl fastq2fasta "workflows/fastq2fasta/fastq2fasta.cwl") diff --git a/scripts/variant-calling-bowtie-bwa-mem.scm b/scripts/variant-calling-bowtie-bwa-mem.scm index 88498f6..5ddc1f6 100644 --- a/scripts/variant-calling-bowtie-bwa-mem.scm +++ b/scripts/variant-calling-bowtie-bwa-mem.scm @@ -35,17 +35,14 @@ (list "samtools" "sort" "-")) (command "samtools_markdup" (list "samtools" "markdup" "-" "-") - #:other '((stdout . "dedup.bam")))) - (list (output "dedup_bam" - #:source "samtools_markdup/stdout"))) + #:other '((stdout . "dedup.bam"))))) (command "samtools_index" - (list "samtools" "index" - (input "dedup_bam")) + (list "samtools" "index" (input "samtools_stdout")) #:outputs (list (output "indexed_dedup_bam" - #:binding '((glob . "$(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")))) |