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Modified docker container to use it from docker hub
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@saramonzon
saramonzon committed Aug 3, 2018
1 parent 0ea2655 commit d768dfd
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Showing 14 changed files with 1,798 additions and 1,527 deletions.
2 changes: 1 addition & 1 deletion conf/docker.config
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ docker {
enabled = true
}
process {
container = 'nextflow-scif'
container = 'buisciii/nextflow-scif:1.0'
executor = 'local'

// To define
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2 changes: 1 addition & 1 deletion conf/singularity.config
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Expand Up @@ -13,7 +13,7 @@ singularity {
}
process {
// Path to container
container = './nextflow-scif.simg'
container = 'buisciii/nextflow-scif:1.0'
executor = 'local'

// To define
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Binary file modified results/bwa/A.sorted.bam
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578 changes: 335 additions & 243 deletions results/bwa/A.stats.txt
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Binary file modified results/bwa/B.sorted.bam
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578 changes: 335 additions & 243 deletions results/bwa/B.stats.txt
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Binary file modified results/bwa/C.sorted.bam
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578 changes: 335 additions & 243 deletions results/bwa/C.stats.txt
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28 changes: 11 additions & 17 deletions results/report.html
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26 changes: 13 additions & 13 deletions results/timeline.html
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Expand Up @@ -82,20 +82,20 @@
function c1(index) { return "#bdbdbd"; }
function c2(index) { return colors[index % 16]; } // <-- note: uses only the first 16 colors

var elapsed="49.5s"
var beginningMillis=1533291036868;
var endingMillis=1533291086396;
var elapsed="10.8s"
var beginningMillis=1533296394915;
var endingMillis=1533296405754;
var data=[
{"label": "makeBWAindex (genome.fa)", "times": [{"starting_time": 1533291037711, "ending_time": 1533291037800, "color":c1(0)}, {"starting_time": 1533291037800, "ending_time": 1533291038291, "color":c2(0), "label": "7.3s \/ 27.5 MB"}, {"starting_time": 1533291038291, "ending_time": 1533291045038, "color":c1(0)}]},
{"label": "mapping (C)", "times": [{"starting_time": 1533291045110, "ending_time": 1533291045138, "color":c1(1)}, {"starting_time": 1533291045138, "ending_time": 1533291046860, "color":c2(1), "label": "16.5s \/ 210.6 MB"}, {"starting_time": 1533291046860, "ending_time": 1533291061587, "color":c1(1)}]},
{"label": "mapping (A)", "times": [{"starting_time": 1533291045134, "ending_time": 1533291045238, "color":c1(1)}, {"starting_time": 1533291045238, "ending_time": 1533291046945, "color":c2(1), "label": "11s \/ 210.6 MB"}, {"starting_time": 1533291046945, "ending_time": 1533291056181, "color":c1(1)}]},
{"label": "mapping (B)", "times": [{"starting_time": 1533291045148, "ending_time": 1533291045241, "color":c1(1)}, {"starting_time": 1533291045241, "ending_time": 1533291046918, "color":c2(1), "label": "8.5s \/ 210.6 MB"}, {"starting_time": 1533291046918, "ending_time": 1533291053644, "color":c1(1)}]},
{"label": "samtools (B)", "times": [{"starting_time": 1533291053661, "ending_time": 1533291053744, "color":c1(2)}, {"starting_time": 1533291053744, "ending_time": 1533291054276, "color":c2(2), "label": "16.7s \/ 877.7 MB"}, {"starting_time": 1533291054276, "ending_time": 1533291070370, "color":c1(2)}]},
{"label": "samtools (A)", "times": [{"starting_time": 1533291056202, "ending_time": 1533291056280, "color":c1(2)}, {"starting_time": 1533291056280, "ending_time": 1533291056849, "color":c2(2), "label": "16.7s \/ 877.7 MB"}, {"starting_time": 1533291056849, "ending_time": 1533291072906, "color":c1(2)}]},
{"label": "samtools (C)", "times": [{"starting_time": 1533291061606, "ending_time": 1533291061686, "color":c1(2)}, {"starting_time": 1533291061686, "ending_time": 1533291062219, "color":c2(2), "label": "12.7s \/ 877.7 MB"}, {"starting_time": 1533291062219, "ending_time": 1533291074267, "color":c1(2)}]},
{"label": "variantCalling (B)", "times": [{"starting_time": 1533291070390, "ending_time": 1533291070406, "color":c1(3)}, {"starting_time": 1533291070406, "ending_time": 1533291070992, "color":c2(3), "label": "9.7s \/ 86.8 MB"}, {"starting_time": 1533291070992, "ending_time": 1533291080065, "color":c1(3)}]},
{"label": "variantCalling (A)", "times": [{"starting_time": 1533291072923, "ending_time": 1533291073005, "color":c1(3)}, {"starting_time": 1533291073005, "ending_time": 1533291073522, "color":c2(3), "label": "12.5s \/ 86.8 MB"}, {"starting_time": 1533291073522, "ending_time": 1533291085413, "color":c1(3)}]},
{"label": "variantCalling (C)", "times": [{"starting_time": 1533291074286, "ending_time": 1533291074366, "color":c1(3)}, {"starting_time": 1533291074366, "ending_time": 1533291074876, "color":c2(3), "label": "8.5s \/ 86.8 MB"}, {"starting_time": 1533291074876, "ending_time": 1533291082736, "color":c1(3)}]}
{"label": "makeBWAindex (genome.fa)", "times": [{"starting_time": 1533296395677, "ending_time": 1533296395697, "color":c1(0)}, {"starting_time": 1533296395697, "ending_time": 1533296396169, "color":c2(0), "label": "571ms \/ 117.2 MB"}, {"starting_time": 1533296396169, "ending_time": 1533296396248, "color":c1(0)}]},
{"label": "mapping (C)", "times": [{"starting_time": 1533296396328, "ending_time": 1533296396348, "color":c1(1)}, {"starting_time": 1533296396348, "ending_time": 1533296398222, "color":c2(1), "label": "1.9s \/ 296.9 MB"}, {"starting_time": 1533296398222, "ending_time": 1533296398274, "color":c1(1)}]},
{"label": "mapping (B)", "times": [{"starting_time": 1533296396342, "ending_time": 1533296396351, "color":c1(1)}, {"starting_time": 1533296396351, "ending_time": 1533296398231, "color":c2(1), "label": "2s \/ 296.9 MB"}, {"starting_time": 1533296398231, "ending_time": 1533296398301, "color":c1(1)}]},
{"label": "mapping (A)", "times": [{"starting_time": 1533296396351, "ending_time": 1533296396449, "color":c1(1)}, {"starting_time": 1533296396449, "ending_time": 1533296398312, "color":c2(1), "label": "1.9s \/ 296.9 MB"}]},
{"label": "samtools (C)", "times": [{"starting_time": 1533296398290, "ending_time": 1533296398308, "color":c1(2)}, {"starting_time": 1533296398308, "ending_time": 1533296398995, "color":c2(2), "label": "746ms \/ 130.2 MB"}, {"starting_time": 1533296398995, "ending_time": 1533296399036, "color":c1(2)}]},
{"label": "samtools (A)", "times": [{"starting_time": 1533296398310, "ending_time": 1533296398401, "color":c1(2)}, {"starting_time": 1533296398401, "ending_time": 1533296399113, "color":c2(2), "label": "772ms \/ 130.2 MB"}]},
{"label": "samtools (B)", "times": [{"starting_time": 1533296398318, "ending_time": 1533296398403, "color":c1(2)}, {"starting_time": 1533296398403, "ending_time": 1533296399118, "color":c2(2), "label": "774ms \/ 130.2 MB"}]},
{"label": "variantCalling (C)", "times": [{"starting_time": 1533296399058, "ending_time": 1533296399062, "color":c1(3)}, {"starting_time": 1533296399062, "ending_time": 1533296399720, "color":c2(3), "label": "5.7s \/ 168.5 MB"}, {"starting_time": 1533296399720, "ending_time": 1533296404763, "color":c1(3)}]},
{"label": "variantCalling (A)", "times": [{"starting_time": 1533296399103, "ending_time": 1533296399182, "color":c1(3)}, {"starting_time": 1533296399182, "ending_time": 1533296399853, "color":c2(3), "label": "741ms \/ 168.6 MB"}]},
{"label": "variantCalling (B)", "times": [{"starting_time": 1533296399123, "ending_time": 1533296399185, "color":c1(3)}, {"starting_time": 1533296399185, "ending_time": 1533296399879, "color":c2(3), "label": "762ms \/ 168.5 MB"}, {"starting_time": 1533296399879, "ending_time": 1533296399885, "color":c1(3)}]}
]


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20 changes: 10 additions & 10 deletions results/trace.txt
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@@ -1,11 +1,11 @@
task_id hash native_id name status exit submit duration realtime %cpu rss vmem rchar wchar
1 60/90aefa 8065 makeBWAindex (genome.fa) COMPLETED 0 2018-08-03 12:10:37.711 7.3s 491ms 0.0% 4.7 MB 27.5 MB 735.4 KB 509 KB
4 5b/ecb3c6 8519 mapping (B) COMPLETED 0 2018-08-03 12:10:45.148 8.5s 1.7s 33.0% 12 MB 210.6 MB 5.9 MB 97 B
2 bf/43e802 8510 mapping (A) COMPLETED 0 2018-08-03 12:10:45.134 11s 1.7s 34.0% 12 MB 210.6 MB 5.9 MB 97 B
3 b8/b3f827 8494 mapping (C) COMPLETED 0 2018-08-03 12:10:45.110 16.5s 1.7s 35.0% 12 MB 210.6 MB 5.9 MB 97 B
5 6c/014889 9968 samtools (B) COMPLETED 0 2018-08-03 12:10:53.661 16.7s 532ms 28.0% 10.8 MB 877.7 MB 2.2 MB 1.6 MB
6 bc/bc3695 10017 samtools (A) COMPLETED 0 2018-08-03 12:10:56.202 16.7s 569ms 30.0% 10.6 MB 877.7 MB 2.2 MB 1.5 MB
7 52/eecd04 10141 samtools (C) COMPLETED 0 2018-08-03 12:11:01.606 12.7s 533ms 28.0% 9.8 MB 877.7 MB 2.2 MB 1.6 MB
8 22/5651f9 11138 variantCalling (B) COMPLETED 0 2018-08-03 12:11:10.390 9.7s 586ms 0.0% 37 MB 86.8 MB 782.8 KB 233.8 KB
10 b6/0af497 11220 variantCalling (C) COMPLETED 0 2018-08-03 12:11:14.286 8.5s 510ms 31.0% 37 MB 86.8 MB 696.6 KB 181.2 KB
9 99/deadc8 11191 variantCalling (A) COMPLETED 0 2018-08-03 12:11:12.923 12.5s 517ms 38.0% 37 MB 86.8 MB 800.9 KB 268.1 KB
1 b2/6b8e52 9955 makeBWAindex (genome.fa) COMPLETED 0 2018-08-03 13:39:55.677 571ms 472ms 8.0% 2.7 MB 117.2 MB 728.4 KB 508.9 KB
3 06/a0d2ce 10055 mapping (C) COMPLETED 0 2018-08-03 13:39:56.328 1.9s 1.9s 57.0% 11.7 MB 296.9 MB 5.9 MB 97 B
2 f6/3af404 10098 mapping (A) COMPLETED 0 2018-08-03 13:39:56.351 1.9s 1.9s 57.0% 11.7 MB 296.9 MB 5.9 MB 97 B
4 c5/49dc3c 10068 mapping (B) COMPLETED 0 2018-08-03 13:39:56.342 2s 1.9s 55.0% 11.7 MB 296.9 MB 5.9 MB 97 B
5 b5/089036 10576 samtools (C) COMPLETED 0 2018-08-03 13:39:58.290 746ms 687ms 37.0% 11 MB 130.2 MB 2.2 MB 2.1 MB
6 38/45a06f 10593 samtools (A) COMPLETED 0 2018-08-03 13:39:58.310 772ms 712ms 39.0% 11 MB 130.2 MB 2.2 MB 2.1 MB
7 69/e3f32a 10610 samtools (B) COMPLETED 0 2018-08-03 13:39:58.318 774ms 715ms 37.0% 11 MB 130.2 MB 2.2 MB 2.1 MB
9 94/5bd822 10975 variantCalling (A) COMPLETED 0 2018-08-03 13:39:59.103 741ms 671ms 34.0% 36.4 MB 168.6 MB 649.9 KB 112.3 KB
10 96/ea9536 10992 variantCalling (B) COMPLETED 0 2018-08-03 13:39:59.123 762ms 694ms 51.0% 36.4 MB 168.5 MB 869.9 KB 314.7 KB
8 1f/df3295 10943 variantCalling (C) COMPLETED 0 2018-08-03 13:39:59.058 5.7s 658ms 36.0% 36.4 MB 168.5 MB 672.4 KB 136.6 KB
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