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-rw-r--r--workflows/fastq2fasta/bam2fasta.cwl65
-rw-r--r--workflows/fastq2fasta/bcftools-concat.cwl24
-rw-r--r--workflows/fastq2fasta/bcftools-consensus.cwl24
-rw-r--r--workflows/fastq2fasta/bcftools-index.cwl23
-rw-r--r--workflows/fastq2fasta/bcftools-norm.cwl32
-rw-r--r--workflows/fastq2fasta/bcftools-view-exclude-ref.cwl23
-rw-r--r--workflows/fastq2fasta/bcftools-view-qc.cwl24
-rw-r--r--workflows/fastq2fasta/bcftools-view.cwl19
-rw-r--r--workflows/fastq2fasta/bwa-index.cwl32
-rw-r--r--workflows/fastq2fasta/bwa-mem.cwl59
-rw-r--r--workflows/fastq2fasta/fastq2fasta-create-bwaindex.cwl41
-rw-r--r--workflows/fastq2fasta/fastq2fasta.cwl61
-rw-r--r--workflows/fastq2fasta/freebayes.cwl25
-rw-r--r--workflows/fastq2fasta/samtools-faidx.cwl39
-rw-r--r--workflows/fastq2fasta/samtools-sort.cwl41
-rw-r--r--workflows/fastq2fasta/samtools-view.cwl63
16 files changed, 595 insertions, 0 deletions
diff --git a/workflows/fastq2fasta/bam2fasta.cwl b/workflows/fastq2fasta/bam2fasta.cwl
new file mode 100644
index 0000000..efe580f
--- /dev/null
+++ b/workflows/fastq2fasta/bam2fasta.cwl
@@ -0,0 +1,65 @@
+# Reference:
+# https://github.com/VGP/vgp-assembly/blob/33cd6236a68a1aee5f282e365dfe6b97e0b4ebb7/pipeline/freebayes-polish/freebayes.sh
+# https://github.com/VGP/vgp-assembly/blob/33cd6236a68a1aee5f282e365dfe6b97e0b4ebb7/pipeline/freebayes-polish/consensus.sh
+class: Workflow
+cwlVersion: v1.1
+id: bam2fasta
+label: bam2fasta
+requirements: []
+
+inputs:
+ bam:
+ type: File
+ fasta:
+ type: File
+ threads:
+ type: int
+ default: 4
+
+outputs:
+ out_fasta:
+ type: File
+ outputSource: bcftools_consensus/out_fasta
+
+steps:
+ freebayes:
+ in:
+ bam: bam
+ ref_fasta: fasta
+ out: [vcf]
+ run: freebayes.cwl
+ bcftools_view_exclude_ref:
+ in:
+ vcf: freebayes/vcf
+ threads: threads
+ out: [bcf]
+ run: bcftools-view-exclude-ref.cwl
+ bcftools_norm:
+ in:
+ ref_fasta: fasta
+ bcf: bcftools_view_exclude_ref/bcf
+ threads: threads
+ out: [normalized_bcf]
+ run: bcftools-norm.cwl
+ bcftools_index_after_normalization:
+ in:
+ bcf: bcftools_norm/normalized_bcf
+ out: [indexed]
+ run: bcftools-index.cwl
+ bcftools_view_qc:
+ in:
+ bcf: bcftools_index_after_normalization/indexed
+ threads: threads
+ out: [vcf]
+ run: bcftools-view-qc.cwl
+ bcftools_index_after_qc:
+ in:
+ bcf: bcftools_view_qc/vcf
+ out: [indexed]
+ run: bcftools-index.cwl
+ bcftools_consensus:
+ in:
+ ref_fasta: fasta
+ vcf: bcftools_index_after_qc/indexed
+ out: [out_fasta]
+ run: bcftools-consensus.cwl
diff --git a/workflows/fastq2fasta/bcftools-concat.cwl b/workflows/fastq2fasta/bcftools-concat.cwl
new file mode 100644
index 0000000..fc33a30
--- /dev/null
+++ b/workflows/fastq2fasta/bcftools-concat.cwl
@@ -0,0 +1,24 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.1
+hints:
+ DockerRequirement:
+ dockerPull: "quay.io/biocontainers/bcftools:1.10.2--hd2cd319_0"
+baseCommand: bcftools
+arguments:
+ - concat
+ - -Ou
+ - -o
+ - $(inputs.output_name)
+ - $(inputs.bcf_files)
+inputs:
+ - id: output_name
+ type: string
+ default: "merged.bcf"
+ - id: bcf_files
+ type: File[]
+outputs:
+ - id: merged_bcf
+ type: File
+ outputBinding:
+ glob: "$(inputs.output_name)"
diff --git a/workflows/fastq2fasta/bcftools-consensus.cwl b/workflows/fastq2fasta/bcftools-consensus.cwl
new file mode 100644
index 0000000..c111792
--- /dev/null
+++ b/workflows/fastq2fasta/bcftools-consensus.cwl
@@ -0,0 +1,24 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.1
+hints:
+ DockerRequirement:
+ dockerPull: "quay.io/biocontainers/bcftools:1.10.2--hd2cd319_0"
+baseCommand: bcftools
+arguments:
+ - consensus
+ - -i'QUAL > 1 && GT="A"'
+ - -Hla
+ - -f
+ - $(inputs.ref_fasta)
+ - $(inputs.vcf)
+inputs:
+ - id: ref_fasta
+ type: File
+ - id: vcf
+ type: File
+ secondaryFiles: [.csi]
+outputs:
+ - id: out_fasta
+ type: stdout
+stdout: sequence.fasta
diff --git a/workflows/fastq2fasta/bcftools-index.cwl b/workflows/fastq2fasta/bcftools-index.cwl
new file mode 100644
index 0000000..396b680
--- /dev/null
+++ b/workflows/fastq2fasta/bcftools-index.cwl
@@ -0,0 +1,23 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.1
+hints:
+ DockerRequirement:
+ dockerPull: "quay.io/biocontainers/bcftools:1.10.2--hd2cd319_0"
+ InitialWorkDirRequirement:
+ listing:
+ - $(inputs.bcf)
+baseCommand: bcftools
+arguments:
+ - index
+ - $(inputs.bcf)
+inputs:
+ - id: bcf
+ type: File
+outputs:
+ - id: indexed
+ type: File
+ outputBinding:
+ glob: "$(inputs.bcf.basename)"
+ secondaryFiles:
+ - .csi
diff --git a/workflows/fastq2fasta/bcftools-norm.cwl b/workflows/fastq2fasta/bcftools-norm.cwl
new file mode 100644
index 0000000..a765e65
--- /dev/null
+++ b/workflows/fastq2fasta/bcftools-norm.cwl
@@ -0,0 +1,32 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.1
+hints:
+ DockerRequirement:
+ dockerPull: "quay.io/biocontainers/bcftools:1.10.2--hd2cd319_0"
+baseCommand: bcftools
+arguments:
+ - norm
+ - -Ob
+ - -f
+ - $(inputs.ref_fasta)
+ - -o
+ - $(inputs.output_name)
+ - --threads
+ - $(inputs.threads)
+ - $(inputs.bcf)
+inputs:
+ - id: ref_fasta
+ type: File
+ - id: output_name
+ type: string
+ default: "normalized.bcf"
+ - id: threads
+ type: int
+ - id: bcf
+ type: File
+outputs:
+ - id: normalized_bcf
+ type: File
+ outputBinding:
+ glob: "$(inputs.output_name)"
diff --git a/workflows/fastq2fasta/bcftools-view-exclude-ref.cwl b/workflows/fastq2fasta/bcftools-view-exclude-ref.cwl
new file mode 100644
index 0000000..849bd88
--- /dev/null
+++ b/workflows/fastq2fasta/bcftools-view-exclude-ref.cwl
@@ -0,0 +1,23 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.1
+hints:
+ DockerRequirement:
+ dockerPull: "quay.io/biocontainers/bcftools:1.10.2--hd2cd319_0"
+baseCommand: bcftools
+arguments:
+ - view
+ - --no-version
+ - -Ou
+ - -e'type=ref'
+ - --threads=$(inputs.threads)
+ - $(inputs.vcf)
+inputs:
+ - id: vcf
+ type: File
+ - id: threads
+ type: int
+outputs:
+ - id: bcf
+ type: stdout
+stdout: $(inputs.vcf.nameroot).without-ref.bcf
diff --git a/workflows/fastq2fasta/bcftools-view-qc.cwl b/workflows/fastq2fasta/bcftools-view-qc.cwl
new file mode 100644
index 0000000..477c596
--- /dev/null
+++ b/workflows/fastq2fasta/bcftools-view-qc.cwl
@@ -0,0 +1,24 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.1
+hints:
+ DockerRequirement:
+ dockerPull: "quay.io/biocontainers/bcftools:1.10.2--hd2cd319_0"
+baseCommand: bcftools
+arguments:
+ - view
+ - -i
+ - 'QUAL>1 && (GT="AA" || GT="Aa")'
+ - -Oz
+ - --threads=$(inputs.threads)
+ - $(inputs.bcf)
+inputs:
+ - id: threads
+ type: int
+ - id: bcf
+ type: File
+ secondaryFiles: [.csi]
+outputs:
+ - id: vcf
+ type: stdout
+stdout: out.changes.vcf.gz
diff --git a/workflows/fastq2fasta/bcftools-view.cwl b/workflows/fastq2fasta/bcftools-view.cwl
new file mode 100644
index 0000000..2d1a51f
--- /dev/null
+++ b/workflows/fastq2fasta/bcftools-view.cwl
@@ -0,0 +1,19 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.1
+hints:
+ DockerRequirement:
+ dockerPull: "quay.io/biocontainers/bcftools:1.10.2--hd2cd319_0"
+baseCommand: bcftools
+arguments:
+ - view
+ - --no-version
+ - -Ou
+ - $(inputs.vcf)
+inputs:
+ - id: vcf
+ type: File
+outputs:
+ - id: bcf
+ type: stdout
+stdout: $(inputs.vcf.nameroot).bcf
diff --git a/workflows/fastq2fasta/bwa-index.cwl b/workflows/fastq2fasta/bwa-index.cwl
new file mode 100644
index 0000000..775ba8d
--- /dev/null
+++ b/workflows/fastq2fasta/bwa-index.cwl
@@ -0,0 +1,32 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.1
+class: CommandLineTool
+doc: string
+requirements:
+ DockerRequirement:
+ dockerPull: quay.io/biocontainers/bwa:0.7.17--h84994c4_5
+ InitialWorkDirRequirement:
+ listing:
+ - $(inputs.input_fasta)
+baseCommand: [bwa, index]
+inputs:
+ input_fasta:
+ type: File
+ label: "input fasta file"
+ inputBinding:
+ position: 1
+outputs:
+ indexed_fasta:
+ type: File
+ outputBinding:
+ glob: $(inputs.input_fasta.basename)
+ secondaryFiles:
+ - .amb
+ - .ann
+ - .bwt
+ - .pac
+ - .sa
+ stdout: stdout
+ stderr: stderr
+stdout: bwa-index-stdout.log
+stderr: bwa-index-stderr.log
diff --git a/workflows/fastq2fasta/bwa-mem.cwl b/workflows/fastq2fasta/bwa-mem.cwl
new file mode 100644
index 0000000..195411c
--- /dev/null
+++ b/workflows/fastq2fasta/bwa-mem.cwl
@@ -0,0 +1,59 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.1
+class: CommandLineTool
+doc: string
+requirements:
+ DockerRequirement:
+ dockerPull: quay.io/biocontainers/bwa:0.7.17--h84994c4_5
+
+baseCommand: [bwa, mem]
+
+inputs:
+ threads:
+ type: int
+ label: "number of threads"
+ default: 4
+ inputBinding:
+ prefix: -t
+ output_sam:
+ type: string
+ label: "sam file to output results to"
+ default: "out.sam"
+ inputBinding:
+ prefix: -o
+ group_header_line:
+ type: string?
+ label: "read group header line such as '@RG\tID:foo\tSM:bar'"
+ inputBinding:
+ prefix: -R
+ index_base:
+ type: File
+ label: "fasta file for index basename"
+ inputBinding:
+ position: 1
+ secondaryFiles:
+ - .amb
+ - .ann
+ - .bwt
+ - .pac
+ - .sa
+ fastq_forward:
+ type: File
+ label: "input fastq file to map (single-end or forward for pair-end)"
+ inputBinding:
+ position: 2
+ fastq_reverse:
+ type: File?
+ label: "input fastq file to map (reverse for pair-end)"
+ inputBinding:
+ position: 3
+
+outputs:
+ output:
+ type: File
+ outputBinding:
+ glob: "$(inputs.output_sam)"
+ stdout: stdout
+ stderr: stderr
+stdout: bwa-mem-stdout.log
+stderr: bwa-mem-stderr.log
diff --git a/workflows/fastq2fasta/fastq2fasta-create-bwaindex.cwl b/workflows/fastq2fasta/fastq2fasta-create-bwaindex.cwl
new file mode 100644
index 0000000..dab7ff2
--- /dev/null
+++ b/workflows/fastq2fasta/fastq2fasta-create-bwaindex.cwl
@@ -0,0 +1,41 @@
+cwlVersion: v1.1
+class: Workflow
+requirements:
+ SubworkflowFeatureRequirement: {}
+hints:
+ ResourceRequirement:
+ ramMin: 3000
+
+inputs:
+ ref_fasta:
+ type: File
+ fastq_forward:
+ type: File
+ fastq_reverse:
+ type: File?
+ threads:
+ type: int
+ default: 4
+
+outputs:
+ out_fasta:
+ type: File
+ outputSource: fastq2fasta/out_fasta
+
+steps:
+ bwa-index:
+ in: {input_fasta: ref_fasta}
+ out: [indexed_fasta]
+ run: bwa-index.cwl
+ samtools-faidx:
+ in: {input_fasta: bwa-index/indexed_fasta}
+ out: [indexed_fasta]
+ run: samtools-faidx.cwl
+ fastq2fasta:
+ in:
+ fastq_forward: fastq_forward
+ fastq_reverse: fastq_reverse
+ ref_fasta: samtools-faidx/indexed_fasta
+ threads: threads
+ out: [out_fasta]
+ run: fastq2fasta.cwl
diff --git a/workflows/fastq2fasta/fastq2fasta.cwl b/workflows/fastq2fasta/fastq2fasta.cwl
new file mode 100644
index 0000000..0cf5c48
--- /dev/null
+++ b/workflows/fastq2fasta/fastq2fasta.cwl
@@ -0,0 +1,61 @@
+cwlVersion: v1.1
+class: Workflow
+requirements:
+ SubworkflowFeatureRequirement: {}
+hints:
+ ResourceRequirement:
+ ramMin: 3000
+
+inputs:
+ fastq_forward: File
+ fastq_reverse: File?
+ ref_fasta:
+ type: File
+ secondaryFiles:
+ - .amb
+ - .ann
+ - .bwt
+ - .pac
+ - .sa
+ - .fai
+ threads:
+ type: int
+ default: 4
+ metadata: File?
+
+outputs:
+ out_fasta:
+ type: File
+ outputSource: bam2fasta/out_fasta
+ out_metadata:
+ type: File?
+ outputSource: metadata
+
+steps:
+ bwa-mem:
+ in:
+ threads: threads
+ fastq_forward: fastq_forward
+ fastq_reverse: fastq_reverse
+ index_base: ref_fasta
+ out: [output]
+ run: bwa-mem.cwl
+ samtools-view:
+ in:
+ threads: threads
+ input_file: bwa-mem/output
+ out: [bam]
+ run: samtools-view.cwl
+ samtools-sort:
+ in:
+ input_bamfile: samtools-view/bam
+ threads: threads
+ out: [sorted_bam]
+ run: samtools-sort.cwl
+ bam2fasta:
+ in:
+ bam: samtools-sort/sorted_bam
+ fasta: ref_fasta
+ threads: threads
+ out: [out_fasta]
+ run: bam2fasta.cwl
diff --git a/workflows/fastq2fasta/freebayes.cwl b/workflows/fastq2fasta/freebayes.cwl
new file mode 100644
index 0000000..1bf9b2f
--- /dev/null
+++ b/workflows/fastq2fasta/freebayes.cwl
@@ -0,0 +1,25 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: v1.1
+hints:
+ DockerRequirement:
+ dockerPull: "quay.io/biocontainers/freebayes:1.3.2--py37hc088bd4_0"
+baseCommand: freebayes
+arguments: [
+ --bam, $(inputs.bam),
+ # --region=$(inputs.contig):1-$(inputs.contig_end)
+ --ploidy, "1",
+ -f, $(inputs.ref_fasta)]
+inputs:
+ - id: bam
+ type: File
+ # - id: contig
+ # type: string
+ # - id: contig_end
+ # type: int
+ - id: ref_fasta
+ type: File
+outputs:
+ - id: vcf
+ type: stdout
+stdout: var.vcf
diff --git a/workflows/fastq2fasta/samtools-faidx.cwl b/workflows/fastq2fasta/samtools-faidx.cwl
new file mode 100644
index 0000000..5196607
--- /dev/null
+++ b/workflows/fastq2fasta/samtools-faidx.cwl
@@ -0,0 +1,39 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+doc: "samtools sort, sort given bam file"
+requirements:
+ DockerRequirement:
+ dockerPull: quay.io/biocontainers/samtools:1.9--h8571acd_11
+ InitialWorkDirRequirement:
+ listing:
+ - $(inputs.input_fasta)
+baseCommand: [samtools, faidx]
+inputs:
+ input_fasta:
+ type: File
+ label: "Input fasta"
+ inputBinding:
+ position: 1
+ secondaryFiles:
+ - .amb
+ - .ann
+ - .bwt
+ - .pac
+ - .sa
+outputs:
+ indexed_fasta:
+ type: File
+ outputBinding:
+ glob: "$(inputs.input_fasta.basename)"
+ secondaryFiles:
+ - .amb
+ - .ann
+ - .bwt
+ - .pac
+ - .sa
+ - .fai
+ stdout: stdout
+ stderr: stderr
+stdout: samtools-sort-stdout.log
+stderr: samtools-sort-stderr.log
diff --git a/workflows/fastq2fasta/samtools-sort.cwl b/workflows/fastq2fasta/samtools-sort.cwl
new file mode 100644
index 0000000..4c6340c
--- /dev/null
+++ b/workflows/fastq2fasta/samtools-sort.cwl
@@ -0,0 +1,41 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+doc: "samtools sort, sort given bam file"
+requirements:
+ DockerRequirement:
+ dockerPull: quay.io/biocontainers/samtools:1.9--h8571acd_11
+baseCommand: [samtools, sort]
+inputs:
+ threads:
+ type: int
+ default: 4
+ inputBinding:
+ prefix: -@
+ tmpfile:
+ type: string
+ default: sort.tmp
+ label: "Write temporary files to PREFIX.nnnn.bam"
+ inputBinding:
+ prefix: -T
+ output_bam:
+ type: string
+ default: aln.sorted.bam
+ label: "Write final output to FILENAME"
+ inputBinding:
+ prefix: -o
+ input_bamfile:
+ type: File
+ label: "Input bamfile"
+ inputBinding:
+ position: 1
+
+outputs:
+ sorted_bam:
+ type: File
+ outputBinding:
+ glob: "$(inputs.output_bam)"
+ stdout: stdout
+ stderr: stderr
+stdout: samtools-sort-stdout.log
+stderr: samtools-sort-stderr.log
diff --git a/workflows/fastq2fasta/samtools-view.cwl b/workflows/fastq2fasta/samtools-view.cwl
new file mode 100644
index 0000000..9f11cc6
--- /dev/null
+++ b/workflows/fastq2fasta/samtools-view.cwl
@@ -0,0 +1,63 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+doc: "samtools view to convert sam format to bam format"
+requirements:
+ DockerRequirement:
+ dockerPull: quay.io/biocontainers/samtools:1.9--h8571acd_11
+baseCommand: [samtools, view]
+inputs:
+ threads:
+ type: int
+ label: "Number of additional threads to use"
+ default: 4
+ inputBinding:
+ prefix: -@
+ output_bam:
+ type: boolean
+ label: "output BAM"
+ default: true
+ inputBinding:
+ prefix: -b
+ output_filename:
+ type: string
+ label: "output file name"
+ default: "aln.bam"
+ inputBinding:
+ prefix: -o
+ input_file:
+ type: File
+ label: "input file"
+ inputBinding:
+ position: 1
+ include_header:
+ type: boolean
+ label: "include the header in the output"
+ default: false
+ inputBinding:
+ prefix: -h
+ ignore_previous_version:
+ type: boolean
+ label: "ignored for compatibility with previous samtools versions"
+ default: false
+ inputBinding:
+ prefix: -S
+ filter_alignments:
+ type: string?
+ label: "Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' (i.e. /^0[0-7]+/) [0]."
+ inputBinding:
+ prefix: -F
+ skip_alignments:
+ type: int?
+ label: "Skip alignments with MAPQ smaller than INT [0]."
+ inputBinding:
+ prefix: -q
+outputs:
+ bam:
+ type: File
+ outputBinding:
+ glob: "$(inputs.output_filename)"
+ stdout: stdout
+ stderr: stderr
+stdout: samtools-view-stdout.log
+stderr: samtools-view-stderr.log