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authorMichael R. Crusoe2020-05-05 13:11:02 +0200
committerMichael R. Crusoe2020-05-05 13:11:02 +0200
commit6599feb6a6f8b488bd2d12fcf532c3b8a917a17f (patch)
treeeb965acc5b93ca9824a5c87786f4aa859be00a73
parent4618a271193fa5cd5cb1e10d6f8acee9c6e8132a (diff)
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move some tools into the shared repo
-rw-r--r--workflows/pangenome-generate/minimap2.cwl23
-rw-r--r--workflows/pangenome-generate/odgi-viz.cwl25
-rw-r--r--workflows/pangenome-generate/odgi_to_rdf.cwl9
-rw-r--r--workflows/pangenome-generate/pangenome-generate.cwl39
-rw-r--r--workflows/pangenome-generate/seqkit-rmdup.cwl37
m---------workflows/tools0
6 files changed, 29 insertions, 104 deletions
diff --git a/workflows/pangenome-generate/minimap2.cwl b/workflows/pangenome-generate/minimap2.cwl
deleted file mode 100644
index bf8eb4c..0000000
--- a/workflows/pangenome-generate/minimap2.cwl
+++ /dev/null
@@ -1,23 +0,0 @@
-cwlVersion: v1.1
-class: CommandLineTool
-inputs:
- readsFA: File
-outputs:
- readsPAF: stdout
-requirements:
- InlineJavascriptRequirement: {}
-hints:
- DockerRequirement:
- dockerPull: "quay.io/biocontainers/minimap2:2.17--h8b12597_1"
- ResourceRequirement:
- coresMin: 8
- coresMax: 32
- ramMin: $(15 * 1024)
- outdirMin: $(Math.ceil(inputs.readsFA.size/(1024*1024*1024) + 20))
-stdout: $(inputs.readsFA.nameroot).paf
-baseCommand: minimap2
-arguments: [-cx, asm20,
- -w, "1",
- -t, $(runtime.cores),
- $(inputs.readsFA),
- $(inputs.readsFA)]
diff --git a/workflows/pangenome-generate/odgi-viz.cwl b/workflows/pangenome-generate/odgi-viz.cwl
deleted file mode 100644
index d440fcb..0000000
--- a/workflows/pangenome-generate/odgi-viz.cwl
+++ /dev/null
@@ -1,25 +0,0 @@
-cwlVersion: v1.1
-class: CommandLineTool
-inputs:
- inputODGI: File
-outputs:
- odgiPNG:
- type: File
- outputBinding:
- glob: $(inputs.inputODGI.nameroot).png
-requirements:
- InlineJavascriptRequirement: {}
-hints:
- DockerRequirement:
- dockerPull: "quay.io/biocontainers/odgi:v0.3--py37h8b12597_0"
- ResourceRequirement:
- coresMin: 4
- ramMin: $(7 * 1024)
- outdirMin: 1
-baseCommand: [odgi, viz]
-arguments: [-i, $(inputs.inputODGI),
- -o, $(inputs.inputODGI.nameroot).png,
- -x, "50000",
- -y, "500",
- -R,
- -P, "4"]
diff --git a/workflows/pangenome-generate/odgi_to_rdf.cwl b/workflows/pangenome-generate/odgi_to_rdf.cwl
index 31ef0c5..96579a3 100644
--- a/workflows/pangenome-generate/odgi_to_rdf.cwl
+++ b/workflows/pangenome-generate/odgi_to_rdf.cwl
@@ -10,10 +10,8 @@ requirements:
ResourceRequirement:
ramMin: $((2 * 1024) + 1)
inputs:
- - id: odgi
- type: File
- - id: output_name
- type: string?
+ odgi: File
+ output_name: string?
stdout: $(inputs.output_name || inputs.odgi.nameroot+'.ttl.xz')
@@ -23,5 +21,4 @@ arguments:
xz, --stdout]
outputs:
- - id: rdf
- type: stdout
+ rdf: stdout
diff --git a/workflows/pangenome-generate/pangenome-generate.cwl b/workflows/pangenome-generate/pangenome-generate.cwl
index 05e3511..51ea6b4 100644
--- a/workflows/pangenome-generate/pangenome-generate.cwl
+++ b/workflows/pangenome-generate/pangenome-generate.cwl
@@ -23,7 +23,7 @@ outputs:
outputSource: buildGraph/odgiGraph
odgiPNG:
type: File
- outputSource: vizGraph/odgiPNG
+ outputSource: vizGraph/graph_image
seqwishGFA:
type: File
outputSource: induceGraph/seqwishGFA
@@ -32,7 +32,7 @@ outputs:
outputSource: odgi2rdf/rdf
readsMergeDedup:
type: File
- outputSource: dedup/readsMergeDedup
+ outputSource: dedup/reads_dedup
mergedMetadata:
type: File
outputSource: mergeMetadata/merged
@@ -50,17 +50,21 @@ steps:
out: [relabeledSeqs, originalLabels]
run: relabel-seqs.cwl
dedup:
- in: {readsFA: relabel/relabeledSeqs}
- out: [readsMergeDedup, dups]
- run: seqkit-rmdup.cwl
+ in: {reads: relabel/relabeledSeqs}
+ out: [reads_dedup, dups]
+ run: ../tools/seqkit/seqkit_rmdup.cwl
overlapReads:
- in: {readsFA: dedup/readsMergeDedup}
- out: [readsPAF]
- run: minimap2.cwl
+ in:
+ target: dedup/reads_dedup
+ query: dedup/reads_dedup
+ outputCIGAR:
+ default: true
+ out: [alignments]
+ run: ../tools/minimap2/minimap2_paf.cwl
induceGraph:
in:
- readsFA: dedup/readsMergeDedup
- readsPAF: overlapReads/readsPAF
+ readsFA: dedup/reads_dedup
+ readsPAF: overlapReads/alignments
out: [seqwishGFA]
run: seqwish.cwl
buildGraph:
@@ -68,9 +72,18 @@ steps:
out: [odgiGraph]
run: odgi-build.cwl
vizGraph:
- in: {inputODGI: buildGraph/odgiGraph}
- out: [odgiPNG]
- run: odgi-viz.cwl
+ in:
+ sparse_graph_index: buildGraph/odgiGraph
+ width:
+ default: 50000
+ height:
+ default: 500
+ path_per_row:
+ default: true
+ path_height:
+ default: 4
+ out: [graph_image]
+ run: ../tools/odgi/odgi_viz.cwl
odgi2rdf:
in: {odgi: buildGraph/odgiGraph}
out: [rdf]
diff --git a/workflows/pangenome-generate/seqkit-rmdup.cwl b/workflows/pangenome-generate/seqkit-rmdup.cwl
deleted file mode 100644
index 071fa66..0000000
--- a/workflows/pangenome-generate/seqkit-rmdup.cwl
+++ /dev/null
@@ -1,37 +0,0 @@
-cwlVersion: v1.1
-class: CommandLineTool
-inputs:
- readsFA: File
-outputs:
- readsMergeDedup:
- type: File
- outputBinding:
- glob: readsMergeDedup.fasta
- dups:
- type: File?
- outputBinding:
- glob: dups.txt
-requirements:
- InlineJavascriptRequirement: {}
-hints:
- DockerRequirement:
- dockerPull: "quay.io/biocontainers/seqkit:0.7.1--0"
- ResourceRequirement:
- coresMin: 8
- coresMax: 32
- ramMin: $(7 * 1024)
- outdirMin: |
- ${
- var sum = 0;
- for (var i = 0; i < inputs.readsFA.length; i++) {
- sum += inputs.readsFA[i].size;
- }
- return (sum/(1024*1024*1024)+1) + 20;
- }
-baseCommand: seqkit
-arguments: [rmdup,
- --by-seq,
- --ignore-case,
- --dup-num-file, dups.txt,
- -o, readsMergeDedup.fasta,
- $(inputs.readsFA)]
diff --git a/workflows/tools b/workflows/tools
-Subproject 45c2d6dab199cb931b28c54863924ff3cf9079c
+Subproject 2d8523e9a86a9504e77d21f8a878d4f8ef2dac4