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🧹 cleanup: nextflow language server error fixes #635

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🧹 cleanup: nextflow language server error fixes #635

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8 changes: 0 additions & 8 deletions main.nf
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2 changes: 1 addition & 1 deletion nf-training/hello.nf
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
#!/usr/bin/env nextflow

params.greeting = 'Hello world!'
greeting_ch = Channel.of(params.greeting)

process SPLITLETTERS {
input:
Expand Down Expand Up @@ -30,6 +29,7 @@ process CONVERTTOUPPER {
}

workflow {
greeting_ch = Channel.of(params.greeting)
letters_ch = SPLITLETTERS(greeting_ch)
results_ch = CONVERTTOUPPER(letters_ch.flatten())
results_ch.view{ it }
Expand Down
2 changes: 1 addition & 1 deletion nf-training/hello_py.nf
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
#!/usr/bin/env nextflow

params.greeting = 'Hello world!'
greeting_ch = Channel.of(params.greeting)

process SPLITLETTERS {
input:
Expand Down Expand Up @@ -36,6 +35,7 @@ process CONVERTTOUPPER {
}

workflow {
greeting_ch = Channel.of(params.greeting)
letters_ch = SPLITLETTERS(greeting_ch)
results_ch = CONVERTTOUPPER(letters_ch.flatten())
results_ch.view{ it }
Expand Down
2 changes: 1 addition & 1 deletion nf-training/modules.hello.nf
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Original file line number Diff line number Diff line change
@@ -1,12 +1,12 @@
#!/usr/bin/env nextflow

params.greeting = 'Hello world!'
greeting_ch = Channel.of(params.greeting)

include { SPLITLETTERS } from './modules.nf'
include { CONVERTTOUPPER } from './modules.nf'

workflow{
greeting_ch = Channel.of(params.greeting)
letters_ch = SPLITLETTERS(greeting_ch)
results_ch = CONVERTTOUPPER(letters_ch.flatten())
results_ch.view{ it }
Expand Down
4 changes: 3 additions & 1 deletion nf-training/script1.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,6 @@ params.reads = "$projectDir/data/ggal/gut_{1,2}.fq"
params.transcriptome_file = "$projectDir/data/ggal/transcriptome.fa"
params.multiqc = "$projectDir/multiqc"

println "reads: $params.reads"
workflow {
println "reads: $params.reads"
}
18 changes: 9 additions & 9 deletions nf-training/script2.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -8,15 +8,6 @@ params.transcriptome_file = "$projectDir/data/ggal/transcriptome.fa"
params.multiqc = "$projectDir/multiqc"
params.outdir = "results"

log.info """\
R N A S E Q - N F P I P E L I N E
===================================
transcriptome: ${params.transcriptome_file}
reads : ${params.reads}
outdir : ${params.outdir}
"""
.stripIndent(true)

/*
* define the `INDEX` process that creates a binary index
* given the transcriptome file
Expand All @@ -35,5 +26,14 @@ process INDEX {
}

workflow {
log.info """\
R N A S E Q - N F P I P E L I N E
===================================
transcriptome: ${params.transcriptome_file}
reads : ${params.reads}
outdir : ${params.outdir}
"""
.stripIndent(true)

index_ch = INDEX(params.transcriptome_file)
}
20 changes: 11 additions & 9 deletions nf-training/script3.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -8,13 +8,15 @@ params.transcriptome_file = "$projectDir/data/ggal/transcriptome.fa"
params.multiqc = "$projectDir/multiqc"
params.outdir = "results"

log.info """\
R N A S E Q - N F P I P E L I N E
===================================
transcriptome: ${params.transcriptome_file}
reads : ${params.reads}
outdir : ${params.outdir}
"""
.stripIndent()
workflow {
log.info """\
R N A S E Q - N F P I P E L I N E
===================================
transcriptome: ${params.transcriptome_file}
reads : ${params.reads}
outdir : ${params.outdir}
"""
.stripIndent()

read_pairs_ch = Channel.fromFilePairs(params.reads)
read_pairs_ch = Channel.fromFilePairs(params.reads)
}
18 changes: 9 additions & 9 deletions nf-training/script4.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -8,15 +8,6 @@ params.transcriptome_file = "$projectDir/data/ggal/transcriptome.fa"
params.multiqc = "$projectDir/multiqc"
params.outdir = "results"

log.info """\
R N A S E Q - N F P I P E L I N E
===================================
transcriptome: ${params.transcriptome_file}
reads : ${params.reads}
outdir : ${params.outdir}
"""
.stripIndent()

/*
* define the `INDEX` process that creates a binary index
* given the transcriptome file
Expand Down Expand Up @@ -49,6 +40,15 @@ process QUANTIFICATION {
}

workflow {
log.info """\
R N A S E Q - N F P I P E L I N E
===================================
transcriptome: ${params.transcriptome_file}
reads : ${params.reads}
outdir : ${params.outdir}
"""
.stripIndent()

Channel
.fromFilePairs(params.reads, checkIfExists: true)
.set { read_pairs_ch }
Expand Down
18 changes: 9 additions & 9 deletions nf-training/script5.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -8,15 +8,6 @@ params.transcriptome_file = "$projectDir/data/ggal/transcriptome.fa"
params.multiqc = "$projectDir/multiqc"
params.outdir = "results"

log.info """\
R N A S E Q - N F P I P E L I N E
===================================
transcriptome: ${params.transcriptome_file}
reads : ${params.reads}
outdir : ${params.outdir}
"""
.stripIndent()

/*
* define the `INDEX` process that creates a binary index
* given the transcriptome file
Expand Down Expand Up @@ -68,6 +59,15 @@ process FASTQC {
}

workflow {
log.info """\
R N A S E Q - N F P I P E L I N E
===================================
transcriptome: ${params.transcriptome_file}
reads : ${params.reads}
outdir : ${params.outdir}
"""
.stripIndent()

Channel
.fromFilePairs(params.reads, checkIfExists: true)
.set { read_pairs_ch }
Expand Down
17 changes: 8 additions & 9 deletions nf-training/script6.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -8,15 +8,6 @@ params.transcriptome_file = "$projectDir/data/ggal/transcriptome.fa"
params.multiqc = "$projectDir/multiqc"
params.outdir = "results"

log.info """\
R N A S E Q - N F P I P E L I N E
===================================
transcriptome: ${params.transcriptome_file}
reads : ${params.reads}
outdir : ${params.outdir}
"""
.stripIndent()

/*
* define the `INDEX` process that creates a binary index
* given the transcriptome file
Expand Down Expand Up @@ -83,6 +74,14 @@ process MULTIQC {
}

workflow {
log.info """\
R N A S E Q - N F P I P E L I N E
===================================
transcriptome: ${params.transcriptome_file}
reads : ${params.reads}
outdir : ${params.outdir}
"""
.stripIndent()
Channel
.fromFilePairs(params.reads, checkIfExists: true)
.set { read_pairs_ch }
Expand Down
20 changes: 10 additions & 10 deletions nf-training/script7.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -7,14 +7,6 @@ params.reads = "$projectDir/data/ggal/gut_{1,2}.fq"
params.transcriptome_file = "$projectDir/data/ggal/transcriptome.fa"
params.multiqc = "$projectDir/multiqc"
params.outdir = "results"
log.info """\
R N A S E Q - N F P I P E L I N E
===================================
transcriptome: ${params.transcriptome_file}
reads : ${params.reads}
outdir : ${params.outdir}
"""
.stripIndent()

/*
* define the `INDEX` process that creates a binary index
Expand Down Expand Up @@ -82,6 +74,14 @@ process MULTIQC {
}

workflow {
log.info """\
R N A S E Q - N F P I P E L I N E
===================================
transcriptome: ${params.transcriptome_file}
reads : ${params.reads}
outdir : ${params.outdir}
"""
.stripIndent()
Channel
.fromFilePairs(params.reads, checkIfExists: true)
.set { read_pairs_ch }
Expand All @@ -90,8 +90,8 @@ workflow {
quant_ch = QUANTIFICATION(index_ch, read_pairs_ch)
fastqc_ch = FASTQC(read_pairs_ch)
MULTIQC(quant_ch.mix(fastqc_ch).collect())
}

workflow.onComplete {
workflow.onComplete {
log.info ( workflow.success ? "\nDone! Open the following report in your browser --> $params.outdir/multiqc_report.html\n" : "Oops .. something went wrong" )
}
}