update processes lesson

HPCBio · Dec 4, 2023 · 7008f11 · 7008f11
1 parent 7e0ea70
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diff --git a/_episodes/05-processes-part1.md b/_episodes/05-processes-part1.md
@@ -151,7 +151,8 @@ workflow {
 > > nextflow.enable.dsl=2
 > >
 > > process SALMON_VERSION {
-> >    
+> >   module "Salmon/1.10.0-IGB-gcc-8.2.0"
+> > 
 > >   script:
 > >   """
 > >   salmon --version
@@ -169,11 +170,11 @@ workflow {
 > > ~~~
 > > {: .language-bash}
 > > ~~~
-> > N E X T F L O W  ~  version 21.04.0
-> > Launching `process.nf` [prickly_gilbert] - revision: 471a79c65c
+> > N E X T F L O W  ~  version 22.09.7-edge
+> > Launching `salmon-version.nf` [prickly_brazil] DSL2 - revision: bba3557897
 > > executor >  local (1)
-> > [56/5e6001] process > SALMON_VERSION [100%] 1 of 1 ✔
-> > salmon 1.5.2
+> > [07/6d4fce] process > SALMON_VERSION [100%] 1 of 1 ✔
+> > salmon 1.10.0
 > > ~~~
 > {: .solution}
 {: .challenge}
@@ -222,6 +223,8 @@ The `script` block can be a simple one line string in quotes e.g.
 nextflow.enable.dsl=2
 
 process PROCESSBAM {
+    module "SAMtools/1.17-IGB-gcc-8.2.0"
+
     script:
     "samtools sort -o ref1.sorted.bam ${projectDir}/data/yeast/bams/ref1.bam"
 }
@@ -241,6 +244,8 @@ For example:
 nextflow.enable.dsl=2
 
 process PROCESSBAM {
+    module "SAMtools/1.17-IGB-gcc-8.2.0"
+
     script:
     """
     samtools sort -o ref1.sorted.bam ${projectDir}/data/yeast/bams/ref1.bam

diff --git a/files/Per-lesson/1-Getting_started.pdf b/files/Per-lesson/1-Getting_started.pdf
diff --git a/files/Per-lesson/3-Workflow_parameterization.pdf b/files/Per-lesson/3-Workflow_parameterization.pdf
diff --git a/files/Per-lesson/4-Channels.pdf b/files/Per-lesson/4-Channels.pdf
diff --git a/files/Per-lesson/5-Processes-pt1.pdf b/files/Per-lesson/5-Processes-pt1.pdf
diff --git a/files/Per-lesson/6-Processes-pt2.pdf b/files/Per-lesson/6-Processes-pt2.pdf