Commit e975e931 authored by peguerin's avatar peguerin
Browse files

cleaning

parent 8f2d0bde
singularity:
ednatools: /entrepot/utils/conteneurs/ednatools.img
obitools: /entrepot/utils/conteneurs/obitools.simg
fichiers:
rapidrun: /entrepot/donnees/edna/LaPerouse/all_samples.tsv
folder_fastq: /entrepot/donnees/edna/LaPerouse/
folder_refdb: /entrepot/donnees/edna/referenceDatabase/
dat:
mamm: ./01_infos/sample_description/Mamm.dat
teleo: ./01_infos/sample_description/Teleo.dat
chond: ./01_infos/sample_description/Chond.dat
vert: ./01_infos/sample_description/Vert.dat
blacklist:
projet:
- dummy_run
run:
- dummy_run
illuminapairedend:
s_min: 40
good_length_samples:
seq_count : 1
seq_length : 1
clean_pcrerr_samples:
r : 0.05
assign_taxon:
bdr:
mamm: /media/superdisk/edna/donnees/reference_database/reference_database_mamm/embl_std
teleo: /media/superdisk/edna/donnees/reference_database/reference_database_teleo/embl_std
chond: /media/superdisk/edna/donnees/reference_database/reference_database_chond/embl_std
vert: /media/superdisk/edna/donnees/reference_database/reference_database_vert/embl_std
fasta:
mamm: /media/superdisk/edna/donnees/reference_database/reference_database_mamm/db_embl_std.fasta
teleo: /media/superdisk/edna/donnees/reference_database/reference_database_teleo/db_embl_std.fasta
chond: /media/superdisk/edna/donnees/reference_database/reference_database_chond/db_embl_std.fasta
vert: /media/superdisk/edna/donnees/reference_database/reference_database_vert/db_embl_std.fasta
singularity:
ednatools: /usr/local/containers/ednatools.simg
obitools: /usr/local/containers/obitools.simg
fichiers:
rapidrun: /media/superdisk/edna/donnees/ngs/LaPerouse/metadata/all_samples.tsv
folder_fastq: /media/superdisk/edna/donnees/ngs/LaPerouse/
dat:
mamm: /media/superdisk/edna/donnees/ngs/LaPerouse/metadata/Mamm.dat
teleo: /media/superdisk/edna/donnees/ngs/LaPerouse/metadata/Teleo.dat
chond: /media/superdisk/edna/donnees/ngs/LaPerouse/metadata/Chond.dat
vert: /media/superdisk/edna/donnees/ngs/LaPerouse/metadata/Vert.dat
blacklist:
projet:
- dummy_run
run:
- dummy_run
illuminapairedend:
s_min: 40
good_length_samples:
seq_count : 1
seq_length_min : 23
clean_pcrerr_samples:
r : 0.05
assign_taxon:
bdr:
mamm: /media/superdisk/edna/donnees/reference_database/reference_database_mamm/embl_std
teleo: /media/superdisk/edna/donnees/reference_database/reference_database_teleo/embl_std
chond: /media/superdisk/edna/donnees/reference_database/reference_database_chond/embl_std
vert: /media/superdisk/edna/donnees/reference_database/reference_database_vert/embl_std
fasta:
mamm: /media/superdisk/edna/donnees/reference_database/reference_database_mamm/db_embl_std.fasta
teleo: /media/superdisk/edna/donnees/reference_database/reference_database_teleo/db_embl_std.fasta
chond: /media/superdisk/edna/donnees/reference_database/reference_database_chond/db_embl_std.fasta
vert: /media/superdisk/edna/donnees/reference_database/reference_database_vert/db_embl_std.fasta
......@@ -2,7 +2,7 @@ singularity:
ednatools: /usr/local/containers/ednatools.simg
obitools: /usr/local/containers/obitools.simg
fichiers:
rapidrun: /home/peguerin/donnees/ngs/testmaleplofakarava/rapidrun_metadata/malpelo_fakarava_all_samples.tsv
rapidrun: /home/peguerin/donnees/ngs/testmaleplofakarava/rapidrun_metadata/malpelo_fakarava_all_samples.csv
folder_fastq: /home/peguerin/donnees/ngs/testmaleplofakarava/runs/
dat:
mamm: /home/peguerin/donnees/ngs/testmaleplofakarava/rapidrun_metadata/Mamm.dat
......
singularity:
ednatools: /usr/local/containers/ednatools.simg
obitools: /usr/local/containers/obitools.simg
fichiers:
rapidrun: /home/peguerin/donnees/ngs/testmaleplofakarava/rapidrun_metadata/malpelo_fakarava_all_samples.tsv
folder_fastq: /home/peguerin/donnees/ngs/testmaleplofakarava/runs/
dat:
mamm: /home/peguerin/donnees/ngs/testmaleplofakarava/rapidrun_metadata/Mamm.dat
teleo: /home/peguerin/donnees/ngs/testmaleplofakarava/rapidrun_metadata/Teleo.dat
chond: /home/peguerin/donnees/ngs/testmaleplofakarava/rapidrun_metadata/Chond.dat
vert: /home/peguerin/donnees/ngs/testmaleplofakarava/rapidrun_metadata/Vert.dat
blacklist:
projet:
- dummy_run
run:
- 180430_SN234_A_L001_AIMI-9
- 180504_SND405_A_L001_AIMI-10
- 180504_SND405_A_L002_AIMI-11
illuminapairedend:
s_min: 40
good_length_samples:
seq_count : 1
seq_length : 30
clean_pcrerr_samples:
r : 0.05
assign_taxon:
bdr:
mamm: /media/superdisk/edna/donnees/reference_database/reference_database_mamm/embl_std
teleo: /media/superdisk/edna/donnees/reference_database/reference_database_teleo/embl_std
chond: /media/superdisk/edna/donnees/reference_database/reference_database_chond/embl_std
vert: /media/superdisk/edna/donnees/reference_database/reference_database_vert/embl_std
fasta:
mamm: /media/superdisk/edna/donnees/reference_database/reference_database_mamm/db_embl_std.fasta
teleo: /media/superdisk/edna/donnees/reference_database/reference_database_teleo/db_embl_std.fasta
chond: /media/superdisk/edna/donnees/reference_database/reference_database_chond/db_embl_std.fasta
vert: /media/superdisk/edna/donnees/reference_database/reference_database_vert/db_embl_std.fasta
singularity:
ednatools: /media/superdisk/utils/conteneurs/ednatools.simg
obitools: /media/superdisk/utils/conteneurs/obitools.simg
fichiers:
rapidrun: 01_infos/all_samples.tsv
folder_fastq: /media/superdisk/edna/donnees/test/tiny_malpelo-fakarava_rapidrun/
folder_refdb: /media/superdisk/edna/donnees/reference_database/ref141/
dat:
mamm: /media/superdisk/edna/donnees/test/tiny_malpelo-fakarava_rapidrun/Mamm.dat
teleo: /media/superdisk/edna/donnees/test/tiny_malpelo-fakarava_rapidrun/Teleo.dat
chond: /media/superdisk/edna/donnees/test/tiny_malpelo-fakarava_rapidrun/Chond.dat
vert: /media/superdisk/edna/donnees/test/tiny_malpelo-fakarava_rapidrun/Vert.dat
blacklist:
projet:
- dummy_run
run:
- 180430_SN234_A_L001_AIMI-9
- 180504_SND405_A_L001_AIMI-10
- 180504_SND405_A_L002_AIMI-11
illuminapairedend:
s_min: 40
good_length_samples:
seq_count : 1
seq_length : 1
clean_pcrerr_samples:
r : 0.05
assign_taxon:
bdr:
mamm: /media/superdisk/edna/donnees/reference_database/reference_database_mamm/embl_std
teleo: /media/superdisk/edna/donnees/reference_database/reference_database_teleo/embl_std
chond: /media/superdisk/edna/donnees/reference_database/reference_database_chond/embl_std
vert: /media/superdisk/edna/donnees/reference_database/reference_database_vert/embl_std
fasta:
mamm: /media/superdisk/edna/donnees/reference_database/reference_database_mamm/db_embl_std.fasta
teleo: /media/superdisk/edna/donnees/reference_database/reference_database_teleo/db_embl_std.fasta
chond: /media/superdisk/edna/donnees/reference_database/reference_database_chond/db_embl_std.fasta
vert: /media/superdisk/edna/donnees/reference_database/reference_database_vert/db_embl_std.fasta
......@@ -2,7 +2,7 @@ singularity:
ednatools: /usr/local/containers/ednatools.simg
obitools: /usr/local/containers/obitools.simg
fichiers:
rapidrun: ../resources/tutorial/tutorial_rapidrun_data/ngs/testmaleplofakarava/rapidrun_metadata/malpelo_fakarava_all_samples.tsv
rapidrun: ../resources/tutorial/tutorial_rapidrun_data/ngs/testmaleplofakarava/rapidrun_metadata/malpelo_fakarava_all_samples.csv
folder_fastq: ../resources/tutorial/tutorial_rapidrun_data/ngs/testmaleplofakarava/runs/
dat:
mamm: ../resources/tutorial/tutorial_rapidrun_data/ngs/testmaleplofakarava/rapidrun_metadata/Mamm.dat
......
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