Merge pull request #4 from MaxUlysse/0.25.3

Update to use Nextflow 0.25.3

Author: maxulysse

.travis.yml

@@ -8,7 +8,7 @@ services:
   - docker
 
 env:
-  - NXF_VER=0.25.0 SGT_VER=2.3.1
+  - NXF_VER=0.25.3 SGT_VER=2.3.1
 
 install:
   - curl -fsSL get.nextflow.io | bash

README.md

@@ -16,13 +16,6 @@ nextflow run MaxUlysse/compile-beamer /
 
 ## Usage with Singularity [![Singularity status][singularity-badge]][singularity-link]
 
-First dowload the container using
-```bash
-singularity pull --name container/compile-beamer-1.5.img shub://MaxUlysse/compile-beamer
-```
-
-Then you can directly use compile-beamer
-
 ```bash
 nextflow run MaxUlysse/compile-beamer /
 -profile singularity /
@@ -35,7 +28,7 @@ nextflow run MaxUlysse/compile-beamer /
 [docker-link]: https://hub.docker.com/r/maxulysse/compile-beamer
 [licence-badge]: https://img.shields.io/github/license/MaxUlysse/compile-beamer.svg
 [licence-link]: https://github.com/MaxUlysse/compile-beamer/blob/master/LICENSE
-[nextflow-badge]: https://img.shields.io/badge/nextflow-%E2%89%A50.25.0-brightgreen.svg
+[nextflow-badge]: https://img.shields.io/badge/nextflow-%E2%89%A50.25.3-brightgreen.svg
 [nextflow-link]: https://www.nextflow.io/
 [singularity-badge]: https://img.shields.io/badge/singularity_hub-automated-blue.svg
 [singularity-link]: https://singularity-hub.org/collections/170/

conf/singularity.config

@@ -11,4 +11,4 @@ singularity {
   enabled = true
 }
 
-process.container = 'container/compile-beamer-1.5.img'
+process.container = 'shub://MaxUlysse/compile-beamer'

main.nf

@@ -25,9 +25,9 @@ Maxime Garcia <[email protected]> [@MaxUlysse]
 ================================================================================
 */
 
-if (!nextflow.version.matches('>= 0.25.0')) {exit 1, "Nextflow version 0.25.0 or greater is needed to run this workflow"}
+if (!nextflow.version.matches('>= 0.25.3')) exit 1, "Nextflow version 0.25.3 or greater is needed to run this workflow"
 
-version = '1.5'
+version = '1.6'
 
 switch (params) {
   case {params.help} :
@@ -39,7 +39,7 @@ switch (params) {
     exit 1
 }
 
-if (!params.tex) {exit 1, 'No tex file, see --help for more information'}
+if (!params.tex) exit 1, 'No tex file, see --help for more information'
 
 pictures = file(params.pictures)
 tex = file(params.tex)
@@ -92,7 +92,7 @@ def helpMessage() {
   // Display help message
   this.compileBeamerMessage()
   log.info "    Usage:"
-  log.info "       nextflow run MaxUlysse/compile-beamer --tex <input.tex> --theme <BTB||KI||SciLifeLab>"
+  log.info "       nextflow run MaxUlysse/compile-beamer --tex <input.tex>"
   log.info "    --tex"
   log.info "      Compile the given tex file"
   log.info "    --help"

nextflow.config

@@ -12,15 +12,16 @@ manifest {
   description = 'Compile Beamer'
 }
 
-process.scratch = true
-
 params {
   help = ''
-  version = ''
-  tex = 'sample.tex'
   pictures = 'pictures'
+  tex = 'sample.tex'
+  version = ''
 }
 
+process.scratch = true
+process.shell = ['/bin/bash', '-euo', 'pipefail']
+
 profiles {
   docker {includeConfig 'conf/docker.config'}
   singularity {includeConfig 'conf/singularity.config'}

scripts/test_docker.sh

@@ -1,4 +1,2 @@
 #!/bin/bash
-set -xeuo pipefail
-
 nextflow run . -profile docker

scripts/test_singularity.sh

@@ -1,7 +1,2 @@
 #!/bin/bash
-
-set -xeuo pipefail
-
-singularity pull --name container/compile-beamer-1.5.img shub://MaxUlysse/compile-beamer
-
-nextflow run . -profile singularity
+NXF_VER=0.25.5-SNAPSHOT nextflow run . -profile singularity