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fix: address docs formatting and add single end workflow ci
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Ryan Routsong
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Dec 12, 2023
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136 changes: 136 additions & 0 deletions
136
.tests/dry_run_out/paired_end/.config/config_job_0.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,136 @@ | ||
| { | ||
| "run_ids": "paired_end", | ||
| "project": "EXP_PROJ_Doe", | ||
| "rnums": [ | ||
| "1", | ||
| "2" | ||
| ], | ||
| "bcl_files": [], | ||
| "sample_sheet": "/gs1/home/routsongrm/git/OpenOmics/weave/.tests/paired_end/paired_end.csv", | ||
| "samples": [ | ||
| { | ||
| "sid": "LIB_04565_01_S1", | ||
| "r1_adapter": "TTACCGAC", | ||
| "r2_adapter": "CGTATTCG" | ||
| }, | ||
| { | ||
| "sid": "LIB_04566_01_S2", | ||
| "r1_adapter": "TCGGATTC", | ||
| "r2_adapter": "TAGTTGCG" | ||
| }, | ||
| { | ||
| "sid": "LIB_04567_01_S3", | ||
| "r1_adapter": "CTGTACCA", | ||
| "r2_adapter": "AGTCTGTG" | ||
| }, | ||
| { | ||
| "sid": "LIB_04568_01_S4", | ||
| "r1_adapter": "TACGGTCT", | ||
| "r2_adapter": "GCAATGGA" | ||
| }, | ||
| { | ||
| "sid": "LIB_04569_01_S5", | ||
| "r1_adapter": "AAGACCGT", | ||
| "r2_adapter": "CAATCGAC" | ||
| }, | ||
| { | ||
| "sid": "LIB_04570_01_S6", | ||
| "r1_adapter": "GAGAGTAC", | ||
| "r2_adapter": "TGCTTCCA" | ||
| }, | ||
| { | ||
| "sid": "LIB_04571_01_S7", | ||
| "r1_adapter": "TAGGAGCT", | ||
| "r2_adapter": "GTTAAGGC" | ||
| }, | ||
| { | ||
| "sid": "LIB_04572_01_S8", | ||
| "r1_adapter": "AGTGACCT", | ||
| "r2_adapter": "CTCCTAGA" | ||
| }, | ||
| { | ||
| "sid": "LIB_04573_01_S9", | ||
| "r1_adapter": "TCTACGCA", | ||
| "r2_adapter": "GGCTATTG" | ||
| }, | ||
| { | ||
| "sid": "LIB_04574_01_S10", | ||
| "r1_adapter": "GCAATTCC", | ||
| "r2_adapter": "TGTTCGAG" | ||
| }, | ||
| { | ||
| "sid": "LIB_04575_01_S11", | ||
| "r1_adapter": "CTCAGAAG", | ||
| "r2_adapter": "AACTTGCC" | ||
| }, | ||
| { | ||
| "sid": "LIB_04576_01_S12", | ||
| "r1_adapter": "GTCCTAAG", | ||
| "r2_adapter": "TGGTAGCT" | ||
| }, | ||
| { | ||
| "sid": "LIB_04577_01_S13", | ||
| "r1_adapter": "GAACGAAG", | ||
| "r2_adapter": "GGTGATTC" | ||
| }, | ||
| { | ||
| "sid": "LIB_04578_01_S14", | ||
| "r1_adapter": "CGAATTGC", | ||
| "r2_adapter": "CACCTTAC" | ||
| } | ||
| ], | ||
| "sids": [ | ||
| "LIB_04565_01_S1", | ||
| "LIB_04566_01_S2", | ||
| "LIB_04567_01_S3", | ||
| "LIB_04568_01_S4", | ||
| "LIB_04569_01_S5", | ||
| "LIB_04570_01_S6", | ||
| "LIB_04571_01_S7", | ||
| "LIB_04572_01_S8", | ||
| "LIB_04573_01_S9", | ||
| "LIB_04574_01_S10", | ||
| "LIB_04575_01_S11", | ||
| "LIB_04576_01_S12", | ||
| "LIB_04577_01_S13", | ||
| "LIB_04578_01_S14" | ||
| ], | ||
| "out_to": "/gs1/home/routsongrm/git/OpenOmics/weave/.tests/dry_run_out/paired_end", | ||
| "demux_input_dir": "/gs1/home/routsongrm/git/OpenOmics/weave/.tests/paired_end", | ||
| "bclconvert": false, | ||
| "demux_data": false, | ||
| "resources": { | ||
| "sif": "/gs1/RTS/OpenOmics/SIFs/", | ||
| "mounts": { | ||
| "kaiju": { | ||
| "to": "/opt/kaiju", | ||
| "from": "/gs1/RTS/OpenOmics/references/Dmux/kaiju/kaiju_db_nr_euk_2023-05-10", | ||
| "mode": "ro" | ||
| }, | ||
| "kraken2": { | ||
| "to": "/opt/kraken2", | ||
| "from": "/gs1/RTS/OpenOmics/references/Dmux/kraken2/k2_pluspfp_20230605", | ||
| "mode": "ro" | ||
| }, | ||
| "fastq_screen": { | ||
| "to": "/fdb/fastq_screen/FastQ_Screen_Genomes", | ||
| "from": "/gs1/RTS/OpenOmics/references/Dmux/FastQ_Screen_Genomes", | ||
| "mode": "ro" | ||
| } | ||
| } | ||
| }, | ||
| "runqc": true, | ||
| "cluster-cancel": "scancel", | ||
| "restart-times": 3, | ||
| "jobscript": "slurm-jobscript.sh", | ||
| "cluster": "slurm-submit.py", | ||
| "cluster-status": "slurm-status.py", | ||
| "max-jobs-per-second": 10, | ||
| "max-status-checks-per-second": 10, | ||
| "local-cores": 1, | ||
| "latency-wait": 120, | ||
| "use-conda": false, | ||
| "use-singularity": true, | ||
| "jobs": 20, | ||
| "printshellcmds": true | ||
| } |
6 changes: 3 additions & 3 deletions
6
.tests/illumnia_demux/RunInfo.xml → .tests/paired_end/RunInfo.xml
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