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-rw-r--r--scripts/fastq2fasta.scm8
-rw-r--r--scripts/variant-calling-bowtie-bwa-mem.scm14
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