move some tools into the shared repo

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