Merge branch 'master' into master

MG-RAST · Aug 5, 2019 · addf690 · addf690
2 parents 4d9f431 + 4ec9d73
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diff --git a/.dockerignore b/.dockerignore
@@ -1,3 +1,6 @@
 *.md
 .git/*
 .gitmodules/*
+CWL/Data/*
+CWL/Inputs/DBs/*
+tmp/*
diff --git a/.gitignore b/.gitignore
@@ -1,11 +1,14 @@
 # git ignore file 
+*.pyc
+.ipynb_checkpoints
 
 # ignore all generated files
 conf/Pipeline_Conf.pm
 conf/env.sh
+CWL/tmp/*
+CWL/Data/Inputs/DBs/*
 
 # binaries
-superblat
 usearch
 
 # ignore files with # and ~

diff --git a/CWL/Data/Baseline/drisee.receipt b/CWL/Data/Baseline/drisee.receipt
@@ -0,0 +1,26 @@
+{
+    "error": {
+        "location": "file:///Users/wltrimbl/git/MG-RAST/pipeline/CWL/Data/Outputs/drisee.error",
+        "basename": "drisee.error",
+        "class": "File",
+        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
+        "size": 0,
+        "path": "/Users/wltrimbl/git/MG-RAST/pipeline/CWL/Data/Outputs/drisee.error"
+    },
+    "info": {
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+        "basename": "drisee.log",
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+        "path": "/Users/wltrimbl/git/MG-RAST/pipeline/CWL/Data/Outputs/drisee.log"
+    },
+    "stats": {
+        "location": "file:///Users/wltrimbl/git/MG-RAST/pipeline/CWL/Data/Outputs/drisee.stats",
+        "basename": "drisee.stats",
+        "class": "File",
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+        "path": "/Users/wltrimbl/git/MG-RAST/pipeline/CWL/Data/Outputs/drisee.stats"
+    }
+}
diff --git a/CWL/Data/Baseline/kmer-tool.receipt b/CWL/Data/Baseline/kmer-tool.receipt
@@ -0,0 +1,29 @@
+{
+    "error": {
+        "location": "file:///Users/wltrimbl/git/MG-RAST/pipeline/CWL/outdir/kmer-tool.error",
+        "basename": "kmer-tool.error",
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+    "stats": {
+        "length": 21,
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+            "location": "file:///Users/wltrimbl/git/MG-RAST/pipeline/CWL/outdir/qc.kmer.21.stats",
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+    "summary": {
+        "location": "file:///Users/wltrimbl/git/MG-RAST/pipeline/CWL/outdir/kmer-tool.log",
+        "basename": "kmer-tool.log",
+        "class": "File",
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+    }
+}
diff --git a/CWL/Inputs/README.md b/CWL/Inputs/README.md
@@ -0,0 +1,45 @@
+# Run Test Data
+```
+cd /CWL/Inputs/DBs
+bash getpredata.sh
+
+mkdir -p /data/assembled
+cd /data/assembled
+cwl-runner --debug --no-container /CWL/Workflows/assembled.workflow.cwl /CWL/Workflows/assembled.job.yaml
+
+mkdir -p /data/metabarcode-fastq
+cd /data/metabarcode-fastq
+cwl-runner --debug --no-container /CWL/Workflows/metabarcode-fastq.workflow.cwl /CWL/Workflows/metabarcode-fastq.job.yaml
+
+mkdir -p /data/metabarcode-fasta
+cd /data/metabarcode-fasta
+cwl-runner --debug --no-container /CWL/Workflows/metabarcode-fasta.workflow.cwl /CWL/Workflows/metabarcode-fasta.job.yaml
+
+mkdir -p /data/amplicon-fastq
+cd /data/amplicon-fastq
+cwl-runner --debug --no-container /CWL/Workflows/amplicon-fastq.workflow.cwl /CWL/Workflows/amplicon-fastq.job.yaml
+
+mkdir -p /data/amplicon-fasta
+cd /data/amplicon-fasta
+cwl-runner --debug --no-container /CWL/Workflows/amplicon-fasta.workflow.cwl /CWL/Workflows/amplicon-fasta.job.yaml
+
+mkdir -p /data/wgs-fastq
+cd /data/wgs-fastq
+cwl-runner --debug --no-container /CWL/Workflows/wgs-fastq.workflow.cwl /CWL/Workflows/wgs-fastq.job.yaml
+
+mkdir -p /data/wgs-fasta
+cd /data/wgs-fasta
+cwl-runner --debug --no-container /CWL/Workflows/wgs-fasta.workflow.cwl /CWL/Workflows/wgs-fasta.job.yaml
+
+mkdir -p /data/wgs-noscreen-fastq
+cd /data/wgs-noscreen-fastq
+cwl-runner --debug --no-container /CWL/Workflows/wgs-noscreen-fastq.workflow.cwl /CWL/Workflows/wgs-noscreen-fastq.job.yaml
+
+mkdir -p /data/wgs-noscreen-fasta
+cd /data/wgs-noscreen-fasta
+cwl-runner --debug --no-container /CWL/Workflows/wgs-noscreen-fasta.workflow.cwl /CWL/Workflows/wgs-noscreen-fasta.job.yaml
+
+mkdir -p /data/wgs-noqc-fasta
+cd /data/wgs-noqc-fasta
+cwl-runner --debug --no-container /CWL/Workflows/wgs-noscreen-fasta.workflow.cwl /CWL/Workflows/wgs-noqc-fasta.job.yaml
+```
diff --git a/CWL/Inputs/sequences.amplicon.fasta b/CWL/Inputs/sequences.amplicon.fasta
diff --git a/CWL/Inputs/sequences.amplicon.fasta.md5 b/CWL/Inputs/sequences.amplicon.fasta.md5
@@ -0,0 +1 @@
+37cbb1f811a144158cec0cbd87d97941
diff --git a/CWL/Inputs/sequences.amplicon.fastq b/CWL/Inputs/sequences.amplicon.fastq
diff --git a/CWL/Inputs/sequences.amplicon.fastq.md5 b/CWL/Inputs/sequences.amplicon.fastq.md5
@@ -0,0 +1 @@
+4ad9d0c5069c55c72e07f7791d61c2f1
diff --git a/CWL/Inputs/sequences.assembled.fasta b/CWL/Inputs/sequences.assembled.fasta
diff --git a/CWL/Inputs/sequences.assembled.fasta.md5 b/CWL/Inputs/sequences.assembled.fasta.md5
@@ -0,0 +1 @@
+0170f1416d1368394317e306a81de172