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edna
snakemake_rapidrun_obitools
Commits
6688a0b5
Commit
6688a0b5
authored
Feb 11, 2021
by
peguerin
Browse files
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parent
ab5d8156
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2
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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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