cleaning

config/config_laperouse_alsace.yaml

-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

config/config_laperouse_marbec.yaml

-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

config/config_marbec_rapdirun_test.yaml

@@ -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

config/config_marbec_rapdirun_test_sdx.yaml

-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

config/config_tiny.yaml

-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

config/config_tutorial_rapidrun.yaml

@@ -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