diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/fastq2fasta.scm | 8 | ||||
| -rw-r--r-- | scripts/variant-calling-bowtie-bwa-mem.scm | 14 |
2 files changed, 7 insertions, 15 deletions
diff --git a/scripts/fastq2fasta.scm b/scripts/fastq2fasta.scm index ef4682c..6fa985c 100644 --- a/scripts/fastq2fasta.scm +++ b/scripts/fastq2fasta.scm @@ -12,7 +12,6 @@ (define ref-fasta (input "ref_fasta" - #:type 'File #:other '((secondary-files . #(".amb" ".ann" ".bwt" ".pac" ".sa"))))) (define output-sam @@ -23,7 +22,6 @@ (define fastq-forward (input "fastq_forward" - #:type 'File #:label "input fastq file to map (single-end or forward for pair-end)")) (define fastq-reverse @@ -58,7 +56,7 @@ #:type 'File #:source "bcftools_norm/stdout"))) (command "bcftools_index_after_normalization" - (list "bcftools" "index" (input "normalized" #:type 'File)) + (list "bcftools" "index" (input "normalized")) #:outputs (list (output "index_after_normalization" #:type 'File #:binding '((glob . "$(inputs.normalized.basename)")) @@ -70,12 +68,11 @@ "-i" "'QUAL > 10 && GT=\"a\"'" "-Oz" "--threads" threads (input "index_after_normalization" - #:type 'File #:other '((secondary-files . #(".csi"))))) #:outputs (list (output "bcftools_view_qc_output_vcf" #:type 'stdout)) #:other '((stdout . "bcftools_view_output.vcf.gz"))) (command "bcftools_index_after_qc" - (list "bcftools" "index" (input "bcftools_view_qc_output_vcf" #:type 'File)) + (list "bcftools" "index" (input "bcftools_view_qc_output_vcf")) #:outputs (list (output "index_after_qc" #:type 'File #:binding '((glob . "$(inputs.bcftools_view_qc_output_vcf.basename)")) @@ -88,7 +85,6 @@ "-i" "'QUAL > 10 && GT=\"a\"'" "-Hla" "-f" ref-fasta (input "index_after_qc" - #:type 'File #:other '((secondary-files . #(".csi")))))) (command "set_sample_id" (list "sed" "s/^>.*/>$(inputs.sample_id)/g") diff --git a/scripts/variant-calling-bowtie-bwa-mem.scm b/scripts/variant-calling-bowtie-bwa-mem.scm index 59c1337..598754b 100644 --- a/scripts/variant-calling-bowtie-bwa-mem.scm +++ b/scripts/variant-calling-bowtie-bwa-mem.scm @@ -3,25 +3,22 @@ (use-modules (ccwl ccwl)) (define fastq-1 - (input "fastq_1" #:type 'File)) + (input "fastq_1")) (define fastq-2 - (input "fastq_2" #:type 'File)) + (input "fastq_2")) (define bowtie2-index (input "bowtie2_index" - #:type 'File #:other '((secondary-files . #(".1.bt2" ".2.bt2" ".3.bt2" ".4.bt2" ".rev.1.bt2" ".rev.2.bt2"))))) (define bwa-mem-index (input "bwa_mem_index" - #:type 'File #:other '((secondary-files . #(".amb" ".ann" ".bwt" ".pac" ".sa"))))) (define reference (input "reference" - #:type 'File #:other '((secondary-files . #(".fai"))))) (define (bam2vcf prefix) @@ -29,7 +26,7 @@ (list (pipeline "samtools" (list (command "samtools_view" (list "samtools" "view" "-h" "-b" "-F" "4" - (input (string-append prefix "_input") #:type 'File))) + (input (string-append prefix "_input")))) (command "samtools_sort" (list "samtools" "sort" "-n")) (command "samtools_fixmate" @@ -44,7 +41,7 @@ #:source "samtools_markdup/stdout"))) (command "samtools_index" (list "samtools" "index" - (input "dedup_bam" #:type 'File)) + (input "dedup_bam")) #:outputs (list (output "indexed_dedup_bam" #:type 'File #:binding '((glob . "$(inputs.dedup_bam.basename)")) @@ -55,7 +52,6 @@ (list (command "freebayes" (list "freebayes" "--ploidy" "1" "--bam" (input "indexed_dedup_bam" - #:type 'File #:other '((secondary-files . #("bai")))) "-f" reference)) (command "bcftools_view" @@ -67,8 +63,8 @@ #:type 'File #:source "bcftools_view/stdout"))) (command "tabix" - (list "tabix" (input "vcf" #:type 'File)) #:outputs (list (output "indexed_vcf" #:type 'File + (list "tabix" (input "vcf")) #:binding '((glob . "$(inputs.vcf.basename)")) #:other '((secondary-files . #(".tbi"))))) #:other `((hints (Initial-work-dir-requirement |