Added --version to main.nf

BU-ISCIII · Aug 8, 2018 · 2297ffa · 2297ffa
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commit 2297ffa
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -22,8 +22,13 @@ jobs:
     working_directory: /tmp/src
     steps:
       - run:
-          name: Install parallel gzip and python3
-          command: apk add --no-cache pigz python3
+          name: Install parallel gzip, python3 and java
+          command: apk add --no-cache pigz python3 java
+      - run:
+          name: Install nextflow
+          command: |
+            wget -qO- https://get.nextflow.io | bash
+            export PATH=$PATH:$PWD/nextflow
       - restore_cache:
           keys:
             - docker-v1-{{ .Branch }}-{{ epoch }}

diff --git a/.gitignore b/.gitignore
@@ -11,4 +11,4 @@ work/
 nextflow
 
 # Ignore results files
-results
+results/
diff --git a/Dockerfile b/Dockerfile
@@ -21,3 +21,4 @@ ENV PATH=${PATH}:/scif/apps/bcftools/bin
 # SciF Entrypoint
 # Disabled because of compatibility with nextflow.
 #ENTRYPOINT ["scif"]
+CMD scif
diff --git a/main.nf b/main.nf
@@ -22,7 +22,7 @@ Pipeline overview:
 def helpMessage() {
     log.info"""
     =========================================
-     BU-ISCIII/nextflow-scif DEMO PIPELINE v${version}
+     BU-ISCIII/nextflow-scif DEMO PIPELINE v${params.ver}
     =========================================
     Usage:
 
@@ -36,20 +36,25 @@ def helpMessage() {
       --outdir						Output dir.
       --help						show this message.
       -profile                      Hardware config to use. standard/docker/singularity. Default: standard.
+      --version						Show pipeline version.
 
     """.stripIndent()
 }
 
-// Pipeline version
-version = '0.1'
-
 // Show help message
 params.help = false
 if (params.help){
     helpMessage()
     exit 0
 }
 
+if (params.version){
+    log.info"""
+    	v${params.ver}
+    """.stripIndent()
+    exit 0
+}
+
 // Default parameters
 params.reads = "$baseDir/data/samples/*.fastq"
 params.genome = "$baseDir/data/genome.fa"

diff --git a/nextflow.config b/nextflow.config
@@ -16,7 +16,7 @@ manifest {
 
 // Global default params, used in configs
 params {
-  version = '0.1' //Pipeline version
+  ver = '1.1' //Pipeline version
   nf_required_version = '0.27.6' //Minimum version of Nextflow required
 
   reads="$baseDir/data/samples/*.fastq"

diff --git a/results/bwa/A.sorted.bam b/results/bwa/A.sorted.bam
diff --git a/results/bwa/A.stats.txt b/results/bwa/A.stats.txt
diff --git a/results/bwa/B.sorted.bam b/results/bwa/B.sorted.bam
diff --git a/results/bwa/B.stats.txt b/results/bwa/B.stats.txt
diff --git a/results/bwa/C.sorted.bam b/results/bwa/C.sorted.bam
diff --git a/results/bwa/C.stats.txt b/results/bwa/C.stats.txt
diff --git a/results/report.html b/results/report.html
diff --git a/results/timeline.html b/results/timeline.html
@@ -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="10.8s"
-var beginningMillis=1533296394915;
-var endingMillis=1533296405754;
+var elapsed="6.1s"
+var beginningMillis=1533729133417;
+var endingMillis=1533729139543;
 var data=[
-{"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)}]}
+{"label": "makeBWAindex (genome.fa)", "times": [{"starting_time": 1533729134045, "ending_time": 1533729134148, "color":c1(0)}, {"starting_time": 1533729134148, "ending_time": 1533729134598, "color":c2(0), "label": "546ms \/ 117.2 MB"}]},
+{"label": "mapping (A)", "times": [{"starting_time": 1533729134662, "ending_time": 1533729134692, "color":c1(1)}, {"starting_time": 1533729134692, "ending_time": 1533729136556, "color":c2(1), "label": "1.9s \/ 296.9 MB"}, {"starting_time": 1533729136556, "ending_time": 1533729136608, "color":c1(1)}]},
+{"label": "mapping (C)", "times": [{"starting_time": 1533729134677, "ending_time": 1533729134741, "color":c1(1)}, {"starting_time": 1533729134741, "ending_time": 1533729136721, "color":c2(1), "label": "2.1s \/ 296.9 MB"}, {"starting_time": 1533729136721, "ending_time": 1533729136806, "color":c1(1)}]},
+{"label": "mapping (B)", "times": [{"starting_time": 1533729134686, "ending_time": 1533729134745, "color":c1(1)}, {"starting_time": 1533729134745, "ending_time": 1533729136686, "color":c2(1), "label": "2s \/ 296.9 MB"}, {"starting_time": 1533729136686, "ending_time": 1533729136705, "color":c1(1)}]},
+{"label": "samtools (A)", "times": [{"starting_time": 1533729136626, "ending_time": 1533729136744, "color":c1(2)}, {"starting_time": 1533729136744, "ending_time": 1533729137341, "color":c2(2), "label": "649ms \/ 130.2 MB"}]},
+{"label": "samtools (B)", "times": [{"starting_time": 1533729136751, "ending_time": 1533729136813, "color":c1(2)}, {"starting_time": 1533729136813, "ending_time": 1533729137470, "color":c2(2), "label": "711ms \/ 130.2 MB"}]},
+{"label": "samtools (C)", "times": [{"starting_time": 1533729136848, "ending_time": 1533729136907, "color":c1(2)}, {"starting_time": 1533729136907, "ending_time": 1533729137538, "color":c2(2), "label": "687ms \/ 130.2 MB"}]},
+{"label": "variantCalling (A)", "times": [{"starting_time": 1533729137326, "ending_time": 1533729137375, "color":c1(3)}, {"starting_time": 1533729137375, "ending_time": 1533729138260, "color":c2(3), "label": "970ms \/ 168.6 MB"}, {"starting_time": 1533729138260, "ending_time": 1533729138296, "color":c1(3)}]},
+{"label": "variantCalling (B)", "times": [{"starting_time": 1533729137512, "ending_time": 1533729137545, "color":c1(3)}, {"starting_time": 1533729137545, "ending_time": 1533729138309, "color":c2(3), "label": "824ms \/ 168.5 MB"}, {"starting_time": 1533729138309, "ending_time": 1533729138336, "color":c1(3)}]},
+{"label": "variantCalling (C)", "times": [{"starting_time": 1533729137554, "ending_time": 1533729137635, "color":c1(3)}, {"starting_time": 1533729137635, "ending_time": 1533729138398, "color":c2(3), "label": "832ms \/ 168.5 MB"}]}
 ]
 
 

diff --git a/results/trace.txt b/results/trace.txt
@@ -1,11 +1 @@
 task_id	hash	native_id	name	status	exit	submit	duration	realtime	%cpu	rss	vmem	rchar	wchar
-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