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Werkflow to Master for RQC #16

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merged 9 commits into from
Jun 10, 2023
Merged

Werkflow to Master for RQC #16

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9fab6d2
proof of concpt rqc workflow
scanon Sep 28, 2022
6609adf
Update rqcfilter.wdl
scanon Oct 11, 2022
08f1f71
Minor updates
scanon Oct 11, 2022
c4d7ed7
Bump version
scanon Oct 11, 2022
8995719
change QC to qc to match schema
scanon Nov 8, 2022
99694be
add task make_info_file. issue#14
Jan 26, 2023
412c67d
fix a url link in README
Jan 26, 2023
38d01c5
update README
Jan 28, 2023
a2752a4
Merge pull request #15 from microbiomedata/make_info
scanon May 11, 2023
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28 changes: 9 additions & 19 deletions README.md
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Expand Up @@ -2,7 +2,7 @@

## Summary

This workflow is a replicate of the [QA protocol](https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/data-preprocessing/) implemented at JGI for Illumina reads and use the program “rqcfilter2” from BBTools(38:96) which implements them as a pipeline.
This workflow is a replicate of the [QA protocol](https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/data-preprocessing/) implemented at JGI for Illumina reads and use the program “rqcfilter2” from BBTools(38:96) which implements them as a pipeline.

## Required Database

Expand Down Expand Up @@ -33,27 +33,17 @@ Description of the files:

1. database path,
2. fastq (illumina paired-end interleaved fastq),
3. output path
4. input_interleaved (boolean)
5. forwards reads fastq file (when input_interleaved is false)
6. reverse reads fastq file (when input_interleaved is false)
7. memory (optional) ex: "jgi_rqcfilter.memory": "35G"
8. threads (optional) ex: "jgi_rqcfilter.threads": "16"
3. project name
4. resource where run the workflow
5. informed_by

```
{
"jgi_rqcfilter.database": "/global/cfs/projectdirs/m3408/aim2/database",
"jgi_rqcfilter.input_files": [
"/global/cfs/cdirs/m3408/ficus/8434.3.102077.AGTTCC.fastq.gz",
"/global/cfs/cdirs/m3408/ficus/8434.1.102069.ACAGTG.fastq.gz",
"/global/cfs/cdirs/m3408/ficus/8434.3.102077.ATGTCA.fastq.gz"
],
"jgi_rqcfilter.outdir": "/global/cfs/cdirs/m3408/ficus_rqcfiltered",
"jgi_rqcfilter.input_interleaved": true,
"jgi_rqcfilter.input_fq1":[],
"jgi_rqcfilter.input_fq2":[],
"jgi_rqcfilter.memory": "35G",
"jgi_rqcfilter.threads": "16"
"nmdc_rqcfilter.database": "/global/cfs/projectdirs/m3408/aim2/database",
"nmdc_rqcfilter.input_files": "/global/cfs/cdirs/m3408/ficus/8434.3.102077.AGTTCC.fastq.gz",
"nmdc_rqcfilter.proj":"nmdc:xxxxxxx",
"nmdc_rqcfilter.resouce":"NERSC -- perlmutter",
"nmdc_rqcfilter.informed_by": "nmdc:xxxxxxxx"
}
```

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20 changes: 5 additions & 15 deletions input.json
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@@ -1,17 +1,7 @@
{
"jgi_rqcfilter.database": "/global/cfs/projectdirs/m3408/aim2/database",
"jgi_rqcfilter.input_files": [
"/global/cfs/cdirs/m3408/ficus/8471.3.103168.CCGTCC.fastq.gz",
"/global/cfs/cdirs/m3408/ficus/8434.1.102069.GCCAAT.fastq.gz",
"/global/cfs/cdirs/m3408/ficus/8573.3.104455.GCCAAT.fastq.gz",
"/global/cfs/cdirs/m3408/ficus/8435.3.102098.CCGTCC.fastq.gz",
"/global/cfs/cdirs/m3408/ficus/8382.5.100461.AGTCAA.fastq.gz",
"/global/cfs/cdirs/m3408/ficus/8434.3.102077.AGTTCC.fastq.gz",
"/global/cfs/cdirs/m3408/ficus/8434.1.102069.ACAGTG.fastq.gz",
"/global/cfs/cdirs/m3408/ficus/8434.3.102077.ATGTCA.fastq.gz"
],
"jgi_rqcfilter.input_fq1":[],
"jgi_rqcfilter.input_fq2":[],
"jgi_rqcfilter.outdir": "/global/cfs/cdirs/m3408/ficus_rqcfiltered",
"jgi_rqcfilter.input_interleaved": true
"nmdc_rqcfilter.database": "/global/cfs/projectdirs/m3408/aim2/database",
"nmdc_rqcfilter.input_files": "/global/cfs/cdirs/m3408/ficus/8434.3.102077.AGTTCC.fastq.gz",
"nmdc_rqcfilter.proj":"nmdc:xxxxxxx",
"nmdc_rqcfilter.resouce":"NERSC -- perlmutter",
"nmdc_rqcfilter.informed_by": "nmdc:xxxxxxxx"
}
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