Commit cfada439 authored by Gael  MILLOT's avatar Gael MILLOT
Browse files

v7.7.0 release: Kraken added and multiQC fixed

parent 005eedc2
...@@ -12,7 +12,7 @@ ...@@ -12,7 +12,7 @@
2022-02-17 14:41:55 2022-02-21 16:52:35
...@@ -46,7 +46,7 @@ NUMBER OF OBS POSITIONS: ...@@ -46,7 +46,7 @@ NUMBER OF OBS POSITIONS:
END TIME: 2022-02-17 14:41:55 END TIME: 2022-02-21 16:52:35
...@@ -132,7 +132,7 @@ loaded via a namespace (and not attached): ...@@ -132,7 +132,7 @@ loaded via a namespace (and not attached):
################################ JOB END ################################ JOB END
TIME: 2022-02-17 14:41:55 TIME: 2022-02-21 16:52:35
TOTAL TIME LAPSE: 0S TOTAL TIME LAPSE: 0S
......
...@@ -12,7 +12,7 @@ ...@@ -12,7 +12,7 @@
2022-02-17 14:42:54 2022-02-21 16:54:14
...@@ -31,7 +31,7 @@ ...@@ -31,7 +31,7 @@
END TIME: 2022-02-17 14:42:56 END TIME: 2022-02-21 16:54:16
...@@ -115,7 +115,7 @@ loaded via a namespace (and not attached): ...@@ -115,7 +115,7 @@ loaded via a namespace (and not attached):
################################ JOB END ################################ JOB END
TIME: 2022-02-17 14:42:56 TIME: 2022-02-21 16:54:16
TOTAL TIME LAPSE: 2S TOTAL TIME LAPSE: 2S
......
...@@ -12,7 +12,7 @@ ...@@ -12,7 +12,7 @@
2022-02-17 14:42:40 2022-02-21 16:53:53
...@@ -31,7 +31,7 @@ ...@@ -31,7 +31,7 @@
END TIME: 2022-02-17 14:42:41 END TIME: 2022-02-21 16:53:54
...@@ -64,8 +64,8 @@ erase.objects TRUE ...@@ -64,8 +64,8 @@ erase.objects TRUE
erase.graphs TRUE erase.graphs TRUE
script logo script logo
run.way SCRIPT run.way SCRIPT
command /usr/lib/R/bin/exec/R,--no-echo,--no-restore,--file=/mnt/c/Users/Gael/Documents/Git_projects/14985_loot/bin/logo.R,--args,test.fastq2_LAGGING_16.stat,20,https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.0.0/cute_little_R_functions.R,logo_report.txt command /usr/lib/R/bin/exec/R,--no-echo,--no-restore,--file=/mnt/c/Users/Gael/Documents/Git_projects/14985_loot/bin/logo.R,--args,test.fastq2_LEADING_0.stat,20,https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.0.0/cute_little_R_functions.R,logo_report.txt
freq test.fastq2_LAGGING_16.stat freq test.fastq2_LEADING_0.stat
insertion_dist 20 insertion_dist 20
cute https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.0.0/cute_little_R_functions.R cute https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.0.0/cute_little_R_functions.R
log logo_report.txt log logo_report.txt
...@@ -114,7 +114,7 @@ loaded via a namespace (and not attached): ...@@ -114,7 +114,7 @@ loaded via a namespace (and not attached):
################################ JOB END ################################ JOB END
TIME: 2022-02-17 14:42:41 TIME: 2022-02-21 16:53:54
TOTAL TIME LAPSE: 2S TOTAL TIME LAPSE: 2S
......
...@@ -12,7 +12,7 @@ ...@@ -12,7 +12,7 @@
2022-02-17 15:44:42 2022-02-21 16:50:59
...@@ -78,7 +78,7 @@ fork and orient ...@@ -78,7 +78,7 @@ fork and orient
END TIME: 2022-02-17 15:44:50 END TIME: 2022-02-21 16:51:06
...@@ -168,7 +168,7 @@ loaded via a namespace (and not attached): ...@@ -168,7 +168,7 @@ loaded via a namespace (and not attached):
################################ JOB END ################################ JOB END
TIME: 2022-02-17 15:44:50 TIME: 2022-02-21 16:51:06
TOTAL TIME LAPSE: 8S TOTAL TIME LAPSE: 8S
......
...@@ -26,6 +26,8 @@ env { ...@@ -26,6 +26,8 @@ env {
//fastq_file="test.fastq.gz" // fastq file name //fastq_file="test.fastq.gz" // fastq file name
// fastq_file="Pool-B2699_S1_L001_R1_001.fastq.gz" // fastq_file="Pool-B2699_S1_L001_R1_001.fastq.gz"
fastq_file="test.fastq2.gz" fastq_file="test.fastq2.gz"
//kraken_db="$baseDir/assets/k2_standard"
kraken_db="/pasteur/zeus/services/p01/banques-prod/prod/rel/kraken_standard/current/kraken/2.1.1/standard/"
//fastq_file="4-4_S1_L001_R1_001.fastq.gz" //fastq_file="4-4_S1_L001_R1_001.fastq.gz"
//primer_fasta="$baseDir/dataset/20200520_adapters_TruSeq_B2699_14985_CL.fasta" //primer_fasta="$baseDir/dataset/20200520_adapters_TruSeq_B2699_14985_CL.fasta"
primer_fasta="$baseDir/dataset/20200520_adapters_TruSeq_B2699_14985_CL.fasta" // list of primers used for the library and used by Alien trimmer to trim the raw reads primer_fasta="$baseDir/dataset/20200520_adapters_TruSeq_B2699_14985_CL.fasta" // list of primers used for the library and used by Alien trimmer to trim the raw reads
...@@ -157,6 +159,7 @@ dag { ...@@ -157,6 +159,7 @@ dag {
singularity { singularity {
enabled = true enabled = true
autoMounts = true // automatically mounts host paths in the executed container autoMounts = true // automatically mounts host paths in the executed container
runOptions = '--no-home'
//runOptions = '--home $HOME:/home/$USER --bind /pasteur' // provide any extra command line options supported by the singularity exec. HEre, fait un bind de tout /pasteur dans /pasteur du container. Sinon pas d accès //runOptions = '--home $HOME:/home/$USER --bind /pasteur' // provide any extra command line options supported by the singularity exec. HEre, fait un bind de tout /pasteur dans /pasteur du container. Sinon pas d accès
cacheDir = 'singularity' // name of the directory where remote Singularity images are stored. When rerun, the exec directly uses these without redownloading them. When using a computing cluster it must be a shared folder accessible to all computing nodes cacheDir = 'singularity' // name of the directory where remote Singularity images are stored. When rerun, the exec directly uses these without redownloading them. When using a computing cluster it must be a shared folder accessible to all computing nodes
} }
...@@ -193,6 +196,13 @@ process { ...@@ -193,6 +196,13 @@ process {
cpus=1 // only used when name = "local" in the executor part above cpus=1 // only used when name = "local" in the executor part above
memory='3G' // only used when name = "local" in the executor part above memory='3G' // only used when name = "local" in the executor part above
} }
if(system_exec == 'slurm'){
withLabel: kraken{
container="evolbioinfo/kraken:v2.0.8-beta"
cpus=20
memory='100G'
}
}
withLabel: fastqc { withLabel: fastqc {
container='evolbioinfo/fastqc:v0.11.8' container='evolbioinfo/fastqc:v0.11.8'
......
task_id hash native_id name status exit submit duration realtime %cpu peak_rss peak_vmem rchar wchar
2 e7/424ee9 7078 Nremove (1) CACHED 0 2022-02-21 16:48:59.622 1.9s 456ms 47.3% 11.9 MB 70.6 MB 16.8 MB 14.5 MB
4 ea/7b204f 8004 trim (1) CACHED 0 2022-02-21 16:49:01.543 3s 2s 45.0% 39.5 MB 5.6 GB 16.4 MB 12 MB
7 05/7707f9 12417 kraken (1) CACHED 0 2022-02-21 16:50:50.338 243ms 13ms 66.7% 0 0 150.9 KB 222 B
6 b2/f558e7 12463 fivep_filtering (1) CACHED 0 2022-02-21 16:50:50.390 3.6s 2.1s 23.6% 9.6 MB 61.4 MB 26 MB 14.3 MB
5 60/1c672d 12498 fastqc1 (1) CACHED 0 2022-02-21 16:50:50.424 6.6s 5.3s 72.7% 170.1 MB 3.1 GB 13.7 MB 1.2 MB
8 ad/7167ce 13950 cutoff (1) CACHED 0 2022-02-21 16:50:54.136 1.8s 713ms 18.2% 9.6 MB 61.3 MB 7 MB 3.9 MB
12 70/2d2062 15986 plot_read_length_fivep_filtering (1) CACHED 0 2022-02-21 16:51:19.005 12.1s 11.4s 70.9% 233.2 MB 2.4 GB 19.1 MB 384.1 KB
10 d5/22bb39 15264 plot_read_length_ini (1) CACHED 0 2022-02-21 16:51:07.033 12s 11.3s 71.0% 233.3 MB 2.4 GB 19.1 MB 387.9 KB
11 d0/cf0991 16707 plot_fivep_filtering_stat (1) CACHED 0 2022-02-21 16:51:31.097 12.9s 12.2s 69.7% 204.7 MB 2.4 GB 19.1 MB 816.6 KB
9 1b/206c3d 13905 fastqc2 (1) CACHED 0 2022-02-21 16:50:54.079 5.9s 5s 72.9% 170.2 MB 3.1 GB 12 MB 1.2 MB
15 5f/0d3993 17430 plot_read_length_cutoff (1) CACHED 0 2022-02-21 16:51:43.966 11.9s 11.2s 72.2% 232.9 MB 2.4 GB 19.1 MB 376.6 KB
14 1c/6da551 18153 bowtie2 (1) CACHED 0 2022-02-21 16:51:55.836 4.3s 3.4s 56.5% 112.8 MB 239.5 MB 35 MB 16.2 MB
18 07/cdefb6 18656 Q20 (1) CACHED 0 2022-02-21 16:52:00.229 1.6s 415ms 18.7% 6.5 MB 43.3 MB 3.2 MB 2.2 MB
13 da/b3f5de 12640 motif CACHED 0 2022-02-21 16:50:50.492 16.5s 15.2s 61.3% 214.2 MB 2.4 GB 48.3 MB 39.7 MB
19 fd/8b7c29 18628 coverage (1) CACHED 0 2022-02-21 16:52:00.202 2s 818ms 16.6% 5.1 MB 44.6 MB 479.7 KB 91 KB
21 ba/201d85 19169 no_soft_clipping (1) CACHED 0 2022-02-21 16:52:02.207 1.4s 261ms 15.7% 3.4 MB 38.4 MB 2.1 MB 1.5 MB
22 87/33da6a 19143 coverage (2) CACHED 0 2022-02-21 16:52:02.184 1.8s 696ms 17.8% 5.1 MB 44.6 MB 335 KB 82.4 KB
23 bf/b61635 19194 duplicate_removal (1) CACHED 0 2022-02-21 16:52:02.227 2.7s 1.7s 25.8% 10.5 MB 68.1 MB 12.9 MB 6.6 MB
24 52/0dcca6 19869 plot_coverage (1) CACHED 0 2022-02-21 16:52:03.976 12.3s 11.5s 71.8% 250.1 MB 2.4 GB 19.1 MB 464.3 KB
26 6a/935039 20289 insertion (1) CACHED 0 2022-02-21 16:52:05.968 1.3s 414ms 21.5% 9.2 MB 65.7 MB 2.5 MB 1.7 MB
25 40/5a38e2 21000 plot_coverage (2) CACHED 0 2022-02-21 16:52:16.315 12.1s 11.5s 72.1% 248.7 MB 2.4 GB 19.1 MB 455.9 KB
28 e9/fc33b5 22327 seq_around_insertion (1) CACHED 0 2022-02-21 16:52:36.135 6.3s 5.6s 72.4% 156.6 MB 2.3 GB 17.9 MB 229.4 KB
27 0e/22a316 21721 coverage (3) CACHED 0 2022-02-21 16:52:28.445 1.4s 554ms 19.1% 5.1 MB 44.6 MB 310.2 KB 82.1 KB
29 7f/d7e8a6 21875 final_insertion_files (1) CACHED 0 2022-02-21 16:52:29.844 6.3s 5.6s 72.7% 158 MB 2.3 GB 18 MB 266 KB
30 2a/e44f96 24160 extract_seq (1) CACHED 0 2022-02-21 16:53:04.615 1.6s 796ms 19.4% 5.7 MB 50.2 MB 9.1 MB 4.5 MB
31 c5/8b8fe1 22776 plot_coverage (3) CACHED 0 2022-02-21 16:52:42.416 12.2s 11.5s 71.8% 247 MB 2.4 GB 19.1 MB 459.1 KB
33 d1/dc5fa6 24516 base_freq (3) CACHED 0 2022-02-21 16:53:06.390 1.6s 94ms 11.6% 0 0 282.4 KB 19.7 KB
35 60/df3018 24432 base_freq (1) CACHED 0 2022-02-21 16:53:06.339 1.5s 91ms 11.9% 0 0 279.6 KB 16.8 KB
34 4c/035712 24398 base_freq (2) CACHED 0 2022-02-21 16:53:06.321 1.4s 92ms 10.1% 0 0 281.7 KB 18.9 KB
36 67/c2d494 24467 base_freq (4) CACHED 0 2022-02-21 16:53:06.357 1.5s 96ms 9.2% 0 0 281.8 KB 19 KB
32 24/2b8bb5 23498 random_insertion (1) CACHED 0 2022-02-21 16:52:54.635 10s 9.3s 72.8% 404.6 MB 2.7 GB 30.7 MB 1.2 MB
40 df/870bbd 27091 logo (3) CACHED 0 2022-02-21 16:53:55.074 7.2s 6.5s 72.4% 203.7 MB 2.4 GB 14.6 MB 882.6 KB
38 10/1ac50f 27594 logo (4) CACHED 0 2022-02-21 16:54:02.325 7.1s 6.4s 72.9% 203.6 MB 2.4 GB 14.6 MB 873.7 KB
37 96/bb8ca7 26534 logo (2) CACHED 0 2022-02-21 16:53:47.934 7.1s 6.5s 73.3% 206 MB 2.4 GB 14.6 MB 1002.2 KB
39 e0/06e292 25972 logo (1) CACHED 0 2022-02-21 16:53:40.746 7.2s 6.4s 72.2% 203.1 MB 2.4 GB 14.6 MB 852.9 KB
42 5f/5e0488 28098 global_logo CACHED 0 2022-02-21 16:54:09.435 7.4s 6.7s 74.7% 202.9 MB 2.4 GB 14.6 MB 850.3 KB
43 da/58faf0 24358 plot_insertion (1) CACHED 0 2022-02-21 16:53:06.266 34.5s 33.5s 76.4% 996.7 MB 3.2 GB 40.3 MB 9.7 MB
3 f6/1ecfa6 1754 report1 COMPLETED 0 2022-02-21 17:49:03.342 1.9s 20ms 8.1% 0 0 104.5 KB 683 B
1 f0/46b009 1727 init COMPLETED 0 2022-02-21 17:49:03.301 2s 14ms 8.2% 0 0 104.1 KB 669 B
16 0f/b22999 1857 backup COMPLETED 0 2022-02-21 17:49:03.544 1.8s 17ms 5.3% 0 0 104.3 KB 518 B
41 ed/5d797b 2065 report2 COMPLETED 0 2022-02-21 17:49:03.897 1.6s 31ms 7.7% 0 0 130.8 KB 1.3 KB
17 73/c80a0a 1889 workflowVersion COMPLETED 0 2022-02-21 17:49:03.604 2.3s 735ms 11.8% 5 MB 38.4 MB 141.5 KB 1.7 KB
20 70/937c17 1933 multiQC COMPLETED 0 2022-02-21 17:49:03.659 7.2s 6s 46.3% 75 MB 85.4 MB 28.3 MB 2.3 MB
44 41/ba2fde 2981 print_report (1) COMPLETED 0 2022-02-21 17:49:11.178 9.7s 9s 57.9% 222.1 MB 1 TB 30.9 MB 11.4 MB
...@@ -12,7 +12,7 @@ ...@@ -12,7 +12,7 @@
2022-02-17 14:42:01 2022-02-21 16:52:22
...@@ -31,7 +31,7 @@ ...@@ -31,7 +31,7 @@
END TIME: 2022-02-17 14:42:07 END TIME: 2022-02-21 16:52:28
...@@ -64,9 +64,9 @@ erase.objects TRUE ...@@ -64,9 +64,9 @@ erase.objects TRUE
erase.graphs TRUE erase.graphs TRUE
script plot_coverage script plot_coverage
run.way SCRIPT run.way SCRIPT
command /usr/lib/R/bin/exec/R,--no-echo,--no-restore,--file=/mnt/c/Users/Gael/Documents/Git_projects/14985_loot/bin/plot_coverage.R,--args,test.fastq2_q20_nodup_mini,dup_read_nb,2320711 2320942,4627368 4627400,5,Ecoli Genome (bp),test.fastq2,https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.0.0/cute_little_R_functions.R,plot_coverage_report.txt command /usr/lib/R/bin/exec/R,--no-echo,--no-restore,--file=/mnt/c/Users/Gael/Documents/Git_projects/14985_loot/bin/plot_coverage.R,--args,test.fastq2_q20_mini,read_nb_after,2320711 2320942,4627368 4627400,5,Ecoli Genome (bp),test.fastq2,https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.0.0/cute_little_R_functions.R,plot_coverage_report.txt
cov test.fastq2_q20_nodup_mini cov test.fastq2_q20_mini
read_nb dup_read_nb read_nb read_nb_after
ori_coord 2320711 2320942 ori_coord 2320711 2320942
ter_coord 4627368 4627400 ter_coord 4627368 4627400
color_coverage 5 color_coverage 5
...@@ -120,7 +120,7 @@ loaded via a namespace (and not attached): ...@@ -120,7 +120,7 @@ loaded via a namespace (and not attached):
################################ JOB END ################################ JOB END
TIME: 2022-02-17 14:42:07 TIME: 2022-02-21 16:52:28
TOTAL TIME LAPSE: 6S TOTAL TIME LAPSE: 6S
...@@ -140,7 +140,7 @@ TOTAL TIME LAPSE: 6S ...@@ -140,7 +140,7 @@ TOTAL TIME LAPSE: 6S
2022-02-17 14:41:22 2022-02-21 16:52:09
...@@ -159,7 +159,7 @@ TOTAL TIME LAPSE: 6S ...@@ -159,7 +159,7 @@ TOTAL TIME LAPSE: 6S
END TIME: 2022-02-17 14:41:29 END TIME: 2022-02-21 16:52:15
...@@ -248,7 +248,7 @@ loaded via a namespace (and not attached): ...@@ -248,7 +248,7 @@ loaded via a namespace (and not attached):
################################ JOB END ################################ JOB END
TIME: 2022-02-17 14:41:29 TIME: 2022-02-21 16:52:15
TOTAL TIME LAPSE: 6S TOTAL TIME LAPSE: 6S
...@@ -268,7 +268,7 @@ TOTAL TIME LAPSE: 6S ...@@ -268,7 +268,7 @@ TOTAL TIME LAPSE: 6S
2022-02-17 14:41:35 2022-02-21 16:52:48
...@@ -287,7 +287,7 @@ TOTAL TIME LAPSE: 6S ...@@ -287,7 +287,7 @@ TOTAL TIME LAPSE: 6S
END TIME: 2022-02-17 14:41:41 END TIME: 2022-02-21 16:52:54
...@@ -320,9 +320,9 @@ erase.objects TRUE ...@@ -320,9 +320,9 @@ erase.objects TRUE
erase.graphs TRUE erase.graphs TRUE
script plot_coverage script plot_coverage
run.way SCRIPT run.way SCRIPT
command /usr/lib/R/bin/exec/R,--no-echo,--no-restore,--file=/mnt/c/Users/Gael/Documents/Git_projects/14985_loot/bin/plot_coverage.R,--args,test.fastq2_q20_mini,read_nb_after,2320711 2320942,4627368 4627400,5,Ecoli Genome (bp),test.fastq2,https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.0.0/cute_little_R_functions.R,plot_coverage_report.txt command /usr/lib/R/bin/exec/R,--no-echo,--no-restore,--file=/mnt/c/Users/Gael/Documents/Git_projects/14985_loot/bin/plot_coverage.R,--args,test.fastq2_q20_nodup_mini,dup_read_nb,2320711 2320942,4627368 4627400,5,Ecoli Genome (bp),test.fastq2,https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.0.0/cute_little_R_functions.R,plot_coverage_report.txt
cov test.fastq2_q20_mini cov test.fastq2_q20_nodup_mini
read_nb read_nb_after read_nb dup_read_nb
ori_coord 2320711 2320942 ori_coord 2320711 2320942
ter_coord 4627368 4627400 ter_coord 4627368 4627400
color_coverage 5 color_coverage 5
...@@ -376,7 +376,7 @@ loaded via a namespace (and not attached): ...@@ -376,7 +376,7 @@ loaded via a namespace (and not attached):
################################ JOB END ################################ JOB END
TIME: 2022-02-17 14:41:41 TIME: 2022-02-21 16:52:54
TOTAL TIME LAPSE: 6S TOTAL TIME LAPSE: 6S
......
...@@ -12,7 +12,7 @@ ...@@ -12,7 +12,7 @@
2022-02-16 20:36:16 2022-02-21 16:51:37
...@@ -31,7 +31,7 @@ ...@@ -31,7 +31,7 @@
END TIME: 2022-02-16 20:36:22 END TIME: 2022-02-21 16:51:43
...@@ -115,7 +115,7 @@ loaded via a namespace (and not attached): ...@@ -115,7 +115,7 @@ loaded via a namespace (and not attached):
################################ JOB END ################################ JOB END
TIME: 2022-02-16 20:36:22 TIME: 2022-02-21 16:51:43
TOTAL TIME LAPSE: 6S TOTAL TIME LAPSE: 6S
......
...@@ -12,7 +12,7 @@ ...@@ -12,7 +12,7 @@
2022-02-17 15:45:07 2022-02-21 16:53:12
...@@ -31,7 +31,7 @@ ...@@ -31,7 +31,7 @@
END TIME: 2022-02-17 15:45:34 END TIME: 2022-02-21 16:53:40
...@@ -122,7 +122,7 @@ loaded via a namespace (and not attached): ...@@ -122,7 +122,7 @@ loaded via a namespace (and not attached):
################################ JOB END ################################ JOB END
TIME: 2022-02-17 15:45:34 TIME: 2022-02-21 16:53:40
TOTAL TIME LAPSE: 28S TOTAL TIME LAPSE: 28S
......
...@@ -12,7 +12,7 @@ ...@@ -12,7 +12,7 @@
2022-02-17 14:41:03 2022-02-21 16:51:49
...@@ -31,7 +31,7 @@ ...@@ -31,7 +31,7 @@
END TIME: 2022-02-17 14:41:08 END TIME: 2022-02-21 16:51:55
...@@ -115,7 +115,7 @@ loaded via a namespace (and not attached): ...@@ -115,7 +115,7 @@ loaded via a namespace (and not attached):
################################ JOB END ################################ JOB END
TIME: 2022-02-17 14:41:08 TIME: 2022-02-21 16:51:55
TOTAL TIME LAPSE: 6S TOTAL TIME LAPSE: 6S
......
...@@ -12,7 +12,7 @@ ...@@ -12,7 +12,7 @@
2022-02-17 14:37:20 2022-02-21 16:51:24
...@@ -31,7 +31,7 @@ ...@@ -31,7 +31,7 @@
END TIME: 2022-02-17 14:37:25 END TIME: 2022-02-21 16:51:30
...@@ -115,7 +115,7 @@ loaded via a namespace (and not attached): ...@@ -115,7 +115,7 @@ loaded via a namespace (and not attached):
################################ JOB END ################################ JOB END
TIME: 2022-02-17 14:37:25 TIME: 2022-02-21 16:51:30