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Commit 6688a0b5 authored by peguerin's avatar peguerin
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change path of files

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config/config_tutorial_classic.yaml
View file @ 6688a0b5
......@@ -4,19 +4,19 @@ singularity:
obitools: /usr/local/containers/obitools.simg
fichiers:
rapidrun : NA
folder_fastq: ../resources/tutorial/tutorial_classic_data/ngs/rhone/runs/
folder_fastq: resources/tutorial/tutorial_classic_data/ngs/rhone/runs/
dat:
161124_SND393_A_L005_GWM-849: ../resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016K_Teleo.dat
161124_SND393_A_L005_GWM-850: ../resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016L_Teleo.dat
161124_SND393_A_L005_GWM-851: ../resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016M_Teleo.dat
161124_SND393_A_L005_GWM-852: ../resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016N_Teleo.dat
161124_SND393_A_L005_GWM-853: ../resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016O_Teleo.dat
161124_SND393_A_L005_GWM-854: ../resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016P_Teleo.dat
161124_SND393_A_L005_GWM-855: ../resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016Q_Teleo.dat
161124_SND393_A_L005_GWM-856: ../resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016R_Teleo.dat
161124_SND393_A_L005_GWM-857: ../resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016S_Teleo.dat
161124_SND393_A_L005_GWM-858: ../resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016T_Teleo.dat
161124_SND393_A_L005_GWM-859: ../resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016U_Teleo.dat
161124_SND393_A_L005_GWM-849: resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016K_Teleo.dat
161124_SND393_A_L005_GWM-850: resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016L_Teleo.dat
161124_SND393_A_L005_GWM-851: resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016M_Teleo.dat
161124_SND393_A_L005_GWM-852: resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016N_Teleo.dat
161124_SND393_A_L005_GWM-853: resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016O_Teleo.dat
161124_SND393_A_L005_GWM-854: resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016P_Teleo.dat
161124_SND393_A_L005_GWM-855: resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016Q_Teleo.dat
161124_SND393_A_L005_GWM-856: resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016R_Teleo.dat
161124_SND393_A_L005_GWM-857: resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016S_Teleo.dat
161124_SND393_A_L005_GWM-858: resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016T_Teleo.dat
161124_SND393_A_L005_GWM-859: resources/tutorial/tutorial_classic_data/ngs/rhone/metadata/MB1016U_Teleo.dat
blacklist:
projet:
- dummy_run
......@@ -32,6 +32,6 @@ clean_pcrerr_samples:
r : 0.05
assign_taxon:
bdr:
teleo: ../resources/tutorial/tutorial_classic_data/bdr/reference_database_teleo/embl_std
teleo: resources/tutorial/tutorial_classic_data/bdr/reference_database_teleo/embl_std
fasta:
teleo: ../resources/tutorial/tutorial_classic_data/bdr/reference_database_teleo/db_embl_std.fasta
teleo: resources/tutorial/tutorial_classic_data/bdr/reference_database_teleo/db_embl_std.fasta
config/config_tutorial_rapidrun.yaml
View file @ 6688a0b5
......@@ -3,13 +3,13 @@ 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.csv
folder_fastq: ../resources/tutorial/tutorial_rapidrun_data/ngs/testmaleplofakarava/runs/
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
teleo: ../resources/tutorial/tutorial_rapidrun_data/ngs/testmaleplofakarava/rapidrun_metadata/Teleo.dat
chond: ../resources/tutorial/tutorial_rapidrun_data/ngs/testmaleplofakarava/rapidrun_metadata/Chond.dat
vert: ../resources/tutorial/tutorial_rapidrun_data/ngs/testmaleplofakarava/rapidrun_metadata/Vert.dat
mamm: resources/tutorial/tutorial_rapidrun_data/ngs/testmaleplofakarava/rapidrun_metadata/Mamm.dat
teleo: resources/tutorial/tutorial_rapidrun_data/ngs/testmaleplofakarava/rapidrun_metadata/Teleo.dat
chond: resources/tutorial/tutorial_rapidrun_data/ngs/testmaleplofakarava/rapidrun_metadata/Chond.dat
vert: resources/tutorial/tutorial_rapidrun_data/ngs/testmaleplofakarava/rapidrun_metadata/Vert.dat
blacklist:
projet:
- dummy_run
......@@ -18,7 +18,7 @@ blacklist:
- 180504_SND405_A_L001_AIMI-10
- 180504_SND405_A_L002_AIMI-11
illuminapairedend:
nb_chunk: 0
nb_chunk: 4
s_min: 40
good_length_samples:
seq_count : 1
......@@ -27,12 +27,12 @@ clean_pcrerr_samples:
r : 0.05
assign_taxon:
bdr:
mamm: ../resources/tutorial/tutorial_rapidrun_data/bdr/reference_database_mamm/embl_std
teleo: ../resources/tutorial/tutorial_rapidrun_data/bdr/reference_database_teleo/embl_std
chond: ../resources/tutorial/tutorial_rapidrun_data/bdr/reference_database_chond/embl_std
vert: ../resources/tutorial/tutorial_rapidrun_data/bdr/reference_database_vert/embl_std
mamm: resources/tutorial/tutorial_rapidrun_data/bdr/reference_database_mamm/embl_std
teleo: resources/tutorial/tutorial_rapidrun_data/bdr/reference_database_teleo/embl_std
chond: resources/tutorial/tutorial_rapidrun_data/bdr/reference_database_chond/embl_std
vert: resources/tutorial/tutorial_rapidrun_data/bdr/reference_database_vert/embl_std
fasta:
mamm: ../resources/tutorial/tutorial_rapidrun_data/bdr/reference_database_mamm/db_embl_std.fasta
teleo: ../resources/tutorial/tutorial_rapidrun_data/bdr/reference_database_teleo/db_embl_std.fasta
chond: ../resources/tutorial/tutorial_rapidrun_data/bdr/reference_database_chond/db_embl_std.fasta
vert: ../resources/tutorial/tutorial_rapidrun_data/bdr/reference_database_vert/db_embl_std.fasta
mamm: resources/tutorial/tutorial_rapidrun_data/bdr/reference_database_mamm/db_embl_std.fasta
teleo: resources/tutorial/tutorial_rapidrun_data/bdr/reference_database_teleo/db_embl_std.fasta
chond: resources/tutorial/tutorial_rapidrun_data/bdr/reference_database_chond/db_embl_std.fasta
vert: resources/tutorial/tutorial_rapidrun_data/bdr/reference_database_vert/db_embl_std.fasta
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