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genotoul-bioinfo
metagWGS
Commits
45908ee0
Commit
45908ee0
authored
Sep 17, 2021
by
MARTIN Pierre
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README.md adding --min_contigs_cpm 1000 threshold option
parent
d08b1899
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functional_tests/README.md
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...
@@ -59,9 +59,12 @@ Create a new directory (project-directory) containing a shell script to be used
...
@@ -59,9 +59,12 @@ Create a new directory (project-directory) containing a shell script to be used
#!/bin/bash
#!/bin/bash
sbatch
-W
-p
workq
-J
metagwgs
--mem
=
6G
\
sbatch
-W
-p
workq
-J
metagwgs
--mem
=
6G
\
--wrap
=
"module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq [work_dir]/metaG/metagwgs/main.nf --step '01_clean_qc,02_assembly,03_filtering,04_structural_annot,05_alignment,06_func_annot,07_taxo_affi' --reads '../metagwgs/test/*_{R1,R2}.fastq.gz' --host_fasta '[work_dir]/human_ref/Homo_sapiens.GRCh38_chr21.fa' --host_bwa_index '[work_dir]/human_ref/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '/bank/kaijudb/kaijudb_refseq_2020-05-25' --taxonomy_dir '[work_dir]/taxonomy' --eggnog_mapper_db_dir '/bank/eggnog-mapper/eggnog-mapper-2.0.4-rf1/data' --
assembly metaspades
--diamond_bank "
[
work_dir]/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd
" -with-report -with-timeline -with-trace -with-dag -resume"
--wrap
=
"module load bioinfo/Nextflow-v21.04.1 ; module load system/singularity-3.7.3 ; nextflow run -profile test_genotoul_workq [work_dir]/metaG/metagwgs/main.nf --step '01_clean_qc,02_assembly,03_filtering,04_structural_annot,05_alignment,06_func_annot,07_taxo_affi' --reads '../metagwgs/test/*_{R1,R2}.fastq.gz' --host_fasta '[work_dir]/human_ref/Homo_sapiens.GRCh38_chr21.fa' --host_bwa_index '[work_dir]/human_ref/Homo_sapiens.GRCh38_chr21.fa.{amb,ann,bwt,pac,sa}' --kaiju_db_dir '/bank/kaijudb/kaijudb_refseq_2020-05-25' --taxonomy_dir '[work_dir]/taxonomy' --eggnog_mapper_db_dir '/bank/eggnog-mapper/eggnog-mapper-2.0.4-rf1/data' --
min_contigs_cpm 1000
--diamond_bank "
[
work_dir]/refseq_bacteria_2021-05-20/refseq_bacteria.dmnd
" -with-report -with-timeline -with-trace -with-dag -resume"
```
```
*In this exemple, [work_dir] = "/home/pmartin2/work"*
*"--min_contigs_cpm 1000" is mandatory to have the same results as exp_dir for step 03_filtering*
Then launch this command:
Then launch this command:
```
```
...
...
functional_tests/__pycache__/functions.cpython-37.pyc
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