update import sha and readmes

microbiomedata · Jul 9, 2024 · 75f6272 · 75f6272
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diff --git a/.github/workflows/create_release.yml b/.github/workflows/create_release.yml
@@ -0,0 +1,30 @@
+name: Create Release
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - 'version.txt'
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/[email protected]
+
+      - name: Read version
+        id: get_version
+        run: |
+          VERSION=$(cat version.txt)
+          echo "VERSION=${VERSION}" >> $GITHUB_ENV
+      
+      - name: Create bundle zip
+        run: zip -r bundle.zip *.wdl
+
+      - name: Create Release
+        run: gh release create ${{ env.VERSION }} metaT_assembly.wdl bundle.zip
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/README.md b/README.md
@@ -1,13 +1,52 @@
 # The Metatranscriptome Assembly Pipeline
 
 ## Summary
-This workflow is developed by Brian Foster at JGI. Original repo can be found (here)[https://code.jgi.doe.gov/BFoster/jgi_meta_wdl/-/tree/master/metatranscriptome].
+This workflow is developed by Brian Foster at JGI. Original repo can be found (here)[https://code.jgi.doe.gov/BFoster/jgi_meta_wdl/-/tree/master/metatranscriptome]. This workflow uses BBTools and SPAdes to assemble QC'ed transcriptomic reads. 
 
 ## Running Workflow in Cromwell
 
+Description of the files:
+ - `.wdl` file: the WDL file for workflow definition
+ - `.json` file: the example input for the workflow
+ - `.conf` file: the conf file for running Cromwell.
+ - `.sh` file: the shell script for running the example workflow
+
+
 ## The Docker image and Dockerfile can be found here
 
+[microbiomedata/bbtools:38.96](https://hub.docker.com/r/microbiomedata/bbtools)
+[bryce911/spades:3.15.2](https://hub.docker.com/r/bryce911/spades)
+[microbiomedata/workflowmeta:1.1.1](https://hub.docker.com/r/microbiomedata/workflowmeta)
+
+
 ## Input files
 
+The inputs for this workflow are as follows:
+
+1. project name / contig prefix
+2. Input fastq
+
+
+```
+{
+  "metatranscriptome_assy.input_files":["./test_data/nmdc_xxxxxxx_filtered.fastq.gz"],
+  "metatranscriptome_assy.proj_id":"nmdc:xxxxxxx"
+}
+```
 
 ## Output files
+
+The output will have one directory named by prefix project name and a bunch of output files, including statistical numbers, status log, and run information. 
+
+The main read count table output is named by prefix.pairedMapped_sorted.bam. 
+
+```
+|-- nmdc_xxxxxxx_bamfiles.tar
+|-- nmdc_xxxxxxx_contigs.fna
+|-- nmdc_xxxxxxx_pairedMapped.sam.gz
+|-- nmdc_xxxxxxx_pairedMapped_sorted.bam
+|-- nmdc_xxxxxxx_readlen.txt
+|-- nmdc_xxxxxxx_scaffolds.fna
+|-- nmdc_xxxxxxx_spades.log
+|-- scaffold_stats.json
+```
diff --git a/input.json b/input.json
@@ -0,0 +1,4 @@
+{
+  "metatranscriptome_assy.input_files":["/expanse/projects/nmdc/edge_app/test/kli/metaT_Assembly/test_data/nmdc_xxxxxxx_filtered.fastq.gz"],
+  "metatranscriptome_assy.proj_id":"nmdc:xxxxxxx"
+}
diff --git a/metaT_assembly.wdl b/metaT_assembly.wdl
@@ -1,7 +1,10 @@
 version 1.0
 
-import "https://code.jgi.doe.gov/BFoster/jgi_meta_wdl/raw/main1.0/metatranscriptome/metatranscriptome_assy_rnaspades.wdl" as http_rnaspades
-import "https://code.jgi.doe.gov/BFoster/jgi_meta_wdl/raw/main1.0/common/mapping.wdl?ref=85b9153ebb0804bec25ca692d0dfa7ccf3b5338c" as mapping
+import "https://code.jgi.doe.gov/BFoster/jgi_meta_wdl/-/raw/main1.0/metatranscriptome/metatranscriptome_assy_rnaspades.wdl?ref=0e589f4dfbb4285089c4c99b422e2eec79185ba6" as http_rnaspades
+import "https://code.jgi.doe.gov/BFoster/jgi_meta_wdl/-/raw/main1.0/common/mapping.wdl?ref=0e589f4dfbb4285089c4c99b422e2eec79185ba6" as mapping
+
+# import "./mapping.wdl" as mapping
+# import "./metatranscriptome_assy_rnaspades.wdl" as http_rnaspades
 
 workflow metatranscriptome_assy {
     input{
@@ -10,7 +13,7 @@ workflow metatranscriptome_assy {
         String prefix=sub(proj_id, ":", "_")
         String bbtools_container = "microbiomedata/bbtools:38.96"
         String spades_container_prod = "bryce911/spades:3.15.2"
-        String worflowmeta_container="microbiomedata/workflowmeta:1.1.1"
+        String workflowmeta_container="microbiomedata/workflowmeta:1.1.1"
     }
 
     call http_rnaspades.readstats_raw {
@@ -68,7 +71,7 @@ workflow metatranscriptome_assy {
         sam = finalize_bams.outsam,
         bam = finalize_bams.outbam,
         asmstats = rename_contig.asmstats,
-        container = worflowmeta_container
+        container = workflowmeta_container
     }
 
     call make_info_file {

diff --git a/shifter.conf b/shifter.conf
@@ -39,7 +39,7 @@ backend {
 			${job_shell} ${docker_script}
         """
 
-        dockerRoot = /global/cfs/projectdirs/m3408/aim2/metagenome/assembly/cromwell-executions
+        dockerRoot = /global/cfs/projectdirs/m3408/aim2/metagenome/metatranscriptome_assy/cromwell-executions
         filesystems {
           local {
             localization: [

diff --git a/test_data/test_interl.fq.gz b/test_data/test_interl.fq.gz
diff --git a/version.txt b/version.txt
@@ -0,0 +1 @@
+v0.0.0