Rubocop.yml excludes being ignored - ruby-on-rails-5

My excludes are being ignored.
.rubocop.yml
Rails:
Enabled: true
Exclude:
- 'db/**/*'
- 'config/**/*'
- 'script/**/*'
- 'bin/{rails,rake}'
- 'vendor/**/*'
- 'spec/fixtures/**/*'
- 'tmp/**/*'
Rubocop Message:
config/environments/development.rb:3:1: C: Metrics/BlockLength: Block
has too many lines. [32/25] Rails.application.configure do ...
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ config/environments/production.rb:3:1:
C: Metrics/BlockLength: Block has too many lines. [29/25]
Rails.application.configure do ...
pre-commit GitHook
#!/usr/bin/env ruby
require 'english'
require 'rubocop'
ADDED_OR_MODIFIED = /A|AM|^M/.freeze
changed_files = `git status --porcelain`.split(/\n/).
select { |file_name_with_status|
file_name_with_status =~ ADDED_OR_MODIFIED
}.
map { |file_name_with_status|
file_name_with_status.split(' ')[1]
}.
select { |file_name|
File.extname(file_name) == '.rb'
}.join(' ')
system("rubocop --force-exclusion -a #{changed_files}") unless changed_files.empty?
status=$CHILD_STATUS.to_s[-1].to_i
if status == 0
system("echo -en '\\033[32mFormatting Passed, Committing...\\033[0;39m\n'")
exit 0
else
system("echo -en '\\033[1;31mCannot commit, formating failing. Use --no-verify to force commit.\\033[0;39m\n'")
exit 1
end

Your configuration file only defines excludes for the Rails department of cops, so it is correct that BlockLength, which is in the Metrics department, still inspects the files.
If what you meant to do was to ignore these files for all cops, you can use:
AllCops:
Exclude:
- 'db/**/*'
- 'config/**/*'
- 'script/**/*'
- 'bin/{rails,rake}'
- 'vendor/**/*'
- 'spec/fixtures/**/*'
- 'tmp/**/*'
Rails:
Enabled: true
Or if you just want to exclude the files for the Metrics cops, substitute AllCops for Metrics in the configuration above.

Related

Nextflow DSL2: how to combine outputs (channels) from multiple processes into input of another process by part of filename?

I'm trying to combine outputs from two separate processes A and B, where each of them outputs multiple files, into input of process C. All file names have in common a chromosome number(for example "chr1"). The process A outputs files: /path/chr1_qc.vcf.gz, /path/chr2_qc.vcf.gz and etc (genotype files).
Process B outputs files: /path/chr1.a.bcf, /path/chr1.b.bcf, /path/chr1.c.bcf.../path/chr2.a.bcf, /path/chr2.b.bcf and etc (region files). And the number of both file-sets could vary each time.
Part of the code:
process A {
module "bcftools/1.16"
publishDir "${params.out_dir}", mode: 'copy', overwrite: true
input:
path vcf
path tbi
output:
path ("${(vcf =~ /chr\d{1,2}/)[0]}_qc.vcf.gz")
script:
"""
bcftools view -R ${params.sites_list} -Oz -o ${(vcf =~ /chr\d{1,2}/)[0]}_qc.vcf.gz ${vcf} //generates QC-ed genome files
tabix -f ${(vcf =~ /chr\d{1,2}/)[0]}_qc.vcf.gz //indexing QC-ed genomes
"""
}
process B {
publishDir "${params.out_dir}", mode: 'copy', overwrite: true
input:
path(vcf)
output:
tuple path("${(vcf =~ /chr\d{1,2}/)[0]}.*.bed")
script:
"""
python split_chr.py ${params.chr_lims} ${vcf} //generates region files
"""
}
process C {
publishDir "${params.out_dir}", mode: 'copy', overwrite: true
input:
tuple path(vcf), path(bed)
output:
path "${bed.SimpleName}.vcf.gz"
script:
"""
bcftools view -R ${bed} -Oz -o ${bed.SimpleName}.vcf.gz ${vcf}
"""
}
workflow {
A(someprocess.out)
B(A.out)
C(combined_AB_files)
}
Process B output.view() output:
[/path/chr1.a.bed, /path/chr1.b.bed]
[/path/chr2.a.bed, /path/chr2.b.bed]
How can I get the process C to receive an input as a channel of tuples (A and B outputs combined by chromosome name) like this:
[ /path/chr1_qc.vcf.gz, /path/chr1.a.bcf ]
[ /path/chr1_qc.vcf.gz, /path/chr1.b.bcf ]
...
[ /path/chr2_qc.vcf.gz, /path/chr2.a.bcf ]
...
I think what you want is the second form of the combine operator, which allows you to combine items that share a matching key using the by parameter. If one or more of your channels are missing a shared key in the first element, you can just use the map operator to produce such a key. To get the desired output, use the transpose operator and specify the index (zero based) of the element to be transposed, again using the by parameter. For example:
workflow {
Channel
.fromPath( './data/*.bed' )
.map { tuple( it.simpleName, it ) }
.groupTuple()
.set { bed_files }
Channel
.fromPath( './data/*_qc.vcf.gz' )
.map { tuple( it.simpleName - ~/_qc$/, it ) }
.combine( bed_files, by: 0 )
.transpose( by: 2 )
.map { chrom, vcf, bed -> tuple( vcf, bed ) }
.view()
}
Results:
$ touch ./data/chr{1..3}.{a..c}.bed
$ touch ./data/chr{1..3}_qc.vcf.gz
$ nextflow run main.nf
N E X T F L O W ~ version 22.10.0
Launching `main.nf` [pedantic_woese] DSL2 - revision: 9c5abfca90
[/data/chr1_qc.vcf.gz, /data/chr1.c.bed]
[/data/chr1_qc.vcf.gz, /data/chr1.a.bed]
[/data/chr1_qc.vcf.gz, /data/chr1.b.bed]
[/data/chr2_qc.vcf.gz, /data/chr2.b.bed]
[/data/chr2_qc.vcf.gz, /data/chr2.a.bed]
[/data/chr2_qc.vcf.gz, /data/chr2.c.bed]
[/data/chr3_qc.vcf.gz, /data/chr3.c.bed]
[/data/chr3_qc.vcf.gz, /data/chr3.b.bed]
[/data/chr3_qc.vcf.gz, /data/chr3.a.bed]
Note that when two or more queue channels are declared as process inputs (like in your process A), the process will block until it receives a value from each input channel. As these are run in parallel and asynchronously, there's no guarantee that items will be emitted in the order that they were received. This can result in mix-ups, where for example, you unexpectedly end up with an index file that belongs to another VCF. Most of the time, what you want is one queue channel and one or more value channels. The section in the docs on multiple input channels explains this quite well in my opinion, and is well worth the time reading if you haven't already. Also, joining and combining channels becomes a lot easier when your processes define tuples in their input and output declarations, where the first element is a key, like a sample name/id. I think you want something something like the following:
params.vcf_files = './data/*.vcf.gz{,.tbi}'
params.sites_list = './data/sites.tsv'
params.chr_lims = './data/file.txt'
params.outdir = './results'
process proc_A {
tag "${sample}: ${indexed_vcf.first()}"
publishDir "${params.outdir}/proc_A", mode: 'copy', overwrite: true
module "bcftools/1.16"
input:
tuple val(sample), path(indexed_vcf)
path sites_list
output:
tuple val(sample), path("${sample}_qc.vcf.gz{,.tbi}")
script:
def vcf = indexed_vcf.first()
"""
bcftools view \\
-R "${sites_list}" \\
-Oz \\
-o "${sample}_qc.vcf.gz" \\
"${vcf}"
bcftools index \\
-t \\
"${sample}_qc.vcf.gz"
"""
}
process proc_B {
tag "${sample}: ${indexed_vcf.first()}"
publishDir "${params.outdir}/proc_B", mode: 'copy', overwrite: true
input:
tuple val(sample), path(indexed_vcf)
path chr_lims
output:
tuple val(sample), path("*.bed")
script:
def vcf = indexed_vcf.first()
"""
split_chr.py "${chr_lims}" "${vcf}"
"""
}
process proc_C {
tag "${sample}: ${indexed_vcf.first()}: ${bed.name}"
publishDir "${params.outdir}/proc_C", mode: 'copy', overwrite: true
input:
tuple val(sample), path(indexed_vcf), path(bed)
output:
tuple val(sample), path("${bed.simpleName}.vcf.gz")
script:
def vcf = indexed_vcf.first()
"""
bcftools view \\
-R "${bed}" \\
-Oz \\
-o "${bed.simpleName}.vcf.gz" \\
"${vcf}"
"""
}
workflow {
vcf_files = Channel.fromFilePairs( params.vcf_files )
sites_list = file( params.sites_list )
chr_lims = file( params.chr_lims )
proc_A( vcf_files, sites_list )
proc_B( proc_A.out, chr_lims )
proc_A.out \
| combine( proc_B.out, by: 0 ) \
| map { sample, indexed_vcf, bed_files ->
bed_list = bed_files instanceof Path ? [bed_files] : bed_files
tuple( sample, indexed_vcf, bed_list )
} \
| transpose( by: 2 ) \
| proc_C \
| view()
}
The above should produce results like:
$ nextflow run main.nf
N E X T F L O W ~ version 22.10.0
Launching `main.nf` [mighty_elion] DSL2 - revision: 5ea25ae72c
executor > local (15)
[b4/08df9d] process > proc_A (foo: foo.vcf.gz) [100%] 3 of 3 ✔
[93/55e467] process > proc_B (foo: foo_qc.vcf.gz) [100%] 3 of 3 ✔
[8b/cd7193] process > proc_C (foo: foo_qc.vcf.gz: b.bed) [100%] 9 of 9 ✔
[bar, ./work/90/53b9c6468ca54bb0f4eeb99ca82eda/a.vcf.gz]
[bar, ./work/24/cca839d5f63ee6988ead96dc9fbe1d/b.vcf.gz]
[bar, ./work/6f/61e1587134e68d2e358998f61f6459/c.vcf.gz]
[baz, ./work/f8/1484e94b9187ba6aae81d68f0a18cf/b.vcf.gz]
[baz, ./work/9c/20578262f5a2c13c6c3b566dc7b7d8/c.vcf.gz]
[baz, ./work/f5/3405b54f81f6f500a3ee4a78f5e6df/a.vcf.gz]
[foo, ./work/39/945fb0d3f375260e75afbc9caebc5d/a.vcf.gz]
[foo, ./work/de/cecd94ff39f204e799cb8e4c4ad46f/c.vcf.gz]
[foo, ./work/8b/cd7193107f6be5472d2e29982e3319/b.vcf.gz]
Also note that third party scripts, like your Python script, can be moved to a folder called bin in the root of your project repository (i.e. the same directory as your main.nf). And if you make your script executable, you will be able to invoke "as-is", i.e. without the need for an absolute path to it.
This can be done with channel operators. Check the code below, with some comments:
workflow {
// Let's start by building channels similar to the ones you described
Channel
.of(file('/path/chr1_qc.vcf.gz'), file('/path/chr2_qc.vcf.gz'))
.set { pAoutput}
Channel
.of(file('/path/chr1.a.bcf'), file('/path/chr1.b.bcf'), file('/path/chr1.c.bcf'),
file('/path/chr2.a.bcf'), file('/path/chr2.b.bcf'), file('/path/chr2.c.bcf'))
.set { pBoutput }
// Now, let's create keys to relate the elements in the two channels
pAoutput
.map { filepath -> [filepath.name.tokenize('_')[0], filepath ] }
.set { pAoutput_tuple }
// The channel now looks like this:
// [chr1, /path/chr1_qc.vcf.gz]
// [chr2, /path/chr2_qc.vcf.gz]
pBoutput
.map { filepath -> [filepath.name.tokenize('.')[0], filepath ] }
.set { pBoutput_tuple }
// And:
// [chr1, /path/chr1.a.bcf]
// [chr1, /path/chr1.b.bcf]
// [chr1, /path/chr1.c.bcf]
// [chr2, /path/chr2.a.bcf]
// [chr2, /path/chr2.b.bcf]
// [chr2, /path/chr2.c.bcf]
// Combine the two channels and group by key
pAoutput_tuple
.mix(pBoutput_tuple)
.groupTuple()
.flatMap { chrom, path_list ->
path_list.split {
it.name.endsWith('.vcf.gz')
}.combinations()
}
.view()
}
You can check the output below:
N E X T F L O W ~ version 22.10.4
Launching `ex.nf` [maniac_pike] DSL2 - revision: f87873ef13
[/path/chr1_qc.vcf.gz, /path/chr1.a.bcf]
[/path/chr1_qc.vcf.gz, /path/chr1.b.bcf]
[/path/chr1_qc.vcf.gz, /path/chr1.c.bcf]
[/path/chr2_qc.vcf.gz, /path/chr2.a.bcf]
[/path/chr2_qc.vcf.gz, /path/chr2.b.bcf]
[/path/chr2_qc.vcf.gz, /path/chr2.c.bcf]

Nextflow: Not all items in channel used by process

I've been struggling to identify why a nextflow (v20.10.00) process is not using all the items in a channel. I want the process to run for each sample bam file (10 in total) and for each chromosome (3 in total).
Here is the creation of the channels and the process:
ref_genome = file( params.RefGen, checkIfExists: true )
ref_dir = ref_genome.getParent()
ref_name = ref_genome.getBaseName()
ref_dict = file( "${ref_dir}/${ref_name}.dict", checkIfExists: true )
ref_index = file( "${ref_dir}/${ref_name}.*.fai", checkIfExists: true )
// Handles reading in data if the previous step is skipped
if( params.Skip_BP ){
Channel
.fromFilePairs("${params.ProcBamDir}/*{bam,bai}") { file -> file.name.replaceAll(/.bam|.bai$/,'') }
.ifEmpty { error "No bams found in ${params.ProcBamDir}" }
.map { ID, files -> tuple(ID, files[0], files[1]) }
.set { processed_bams }
}
// Setting up the chromosome channel
if( params.Chroms == "" ){
// Defaulting to using all chromosomes
chromosomes_ch = Channel
.from("AgamP4_2L", "AgamP4_2R", "AgamP4_3L", "AgamP4_3R", "AgamP4_X", "AgamP4_Y_unplaced", "AgamP4_UNKN")
println "No chromosomes specified, using all major chromosomes: AgamP4_2L, AgamP4_2R, AgamP4_3L, AgamP4_3R, AgamP4_X, AgamP4_Y_unplaced, AgamP4_UNKN"
} else {
// User option to choose which chromosome will be used
// This worked with the following syntax nextflow run testing.nf --profile imperial --Chroms "AgamP4_3R,AgamP4_2L"
chrs = params.Chroms.split(",")
chromosomes_ch = Channel
.from( chrs )
println "User defined chromosomes set: ${params.Chroms}"
}
process DNA_HCG {
errorStrategy { sleep(Math.pow(2, task.attempt) * 600 as long); return 'retry' }
maxRetries 3
maxForks params.HCG_Forks
tag { SampleID+"-"+chrom }
executor = 'pbspro'
clusterOptions = "-lselect=1:ncpus=${params.HCG_threads}:mem=${params.HCG_memory}gb:mpiprocs=1:ompthreads=${params.HCG_threads} -lwalltime=${params.HCG_walltime}:00:00"
publishDir(
path: "${params.HCDir}",
mode: 'copy',
)
input:
each chrom from chromosomes_ch
set SampleID, path(bam), path(bai) from processed_bams
path ref_genome
path ref_dict
path ref_index
output:
tuple chrom, path("${SampleID}-${chrom}.vcf") into HCG_ch
path("${SampleID}-${chrom}.vcf.idx") into idx_ch
beforeScript 'module load anaconda3/personal; source activate NF_GATK'
script:
"""
if [ ! -d tmp ]; then mkdir tmp; fi
taskset -c 0-${params.HCG_threads} gatk --java-options \"-Xmx${params.HCG_memory}G -XX:+UseParallelGC -XX:ParallelGCThreads=${params.HCG_threads}\" HaplotypeCaller \\
--tmp-dir tmp/ \\
--pair-hmm-implementation AVX_LOGLESS_CACHING_OMP \\
--native-pair-hmm-threads ${params.HCG_threads} \\
-ERC GVCF \\
-L ${chrom} \\
-R ${ref_genome} \\
-I ${bam} \\
-O ${SampleID}-${chrom}.vcf ${params.GVCF_args}
"""
}
But for reasons I cannot figure out, nextflow only creates 3 jobs: [d8/45499b] process > DNA_HCG (0_wt5_BP-CM029350.1) [ 0%] 0 of 3
I thought maybe it was because it only took the first sample and then one process for each chromosome. Though I doubted this since the code works for a different reference genome correctly. Regardless, I adjusted the input channels:
processed_bams
.combine(chromosomes_ch)
.set { HCG_in }
and
input:
set SampleID, path(bam), path(bai), chrom from HCG_in
But this resulted in only a single job being created: [6e/78b070] process > DNA_HCG (0_wt10_BP-CM029350.1) [ 0%] 0 of 1
Confusingly, when i use HCG_in.view() there are 30 items. And to further confuse me the correct number of jobs comes from the following code:
chrs = params.Chroms.split(",")
chromosomes_ch = Channel
.from(chrs)
Channel
.fromFilePairs("${params.ProcBamDir}/*{bam,bai}") { file -> file.name.replaceAll(/.bam|.bai$/,'') }
.ifEmpty { error "No bams found in ${params.ProcBamDir}" }
.map { ID, files -> tuple(ID, files[0], files[1]) }
.set { processed_bams }
process HCG {
executor 'local'
input:
each chrom from chromosomes_ch
set SampleID, path(bam), path(bai) from processed_bams
//set SampleID, path(bam), path(bai), chrom from HCG_in
script:
"""
echo "${SampleID} - ${chrom}"
"""
}
Output: [75/c1c25a] process > HCG (27) [100%] 30 of 30 ✔
I'm hoping I've just missed something obvious, but I cannot see it at the moment. Thanks in advance for the help.
Issues like this almost always involve the use of multiple input channels:
When two or more channels are declared as process inputs, the process
stops until there’s a complete input configuration ie. it receives an
input value from all the channels declared as input.
Your initial assessment was correct. However, the reason only three processes were run (i.e. one sample for each of the three chromosomes), is because this line (probably) returned a list (i.e. a java LinkedList) containing a single element, and lists behave like queue channels:
ref_index = file( "${ref_dir}/${ref_name}.*.fai", checkIfExists: true )
You might have expected this to return a UnixPath. Ultimately, the solution is to ensure ref_index is value channel.

Overriding Nextflow Parameters with Commandline Arguments

Given the following nextflow.config:
google {
project = "cool-project"
region = "europe-west4"
lifeSciences {
bootDiskSize = "200 GB"
debug = true
preemptible = true
}
}
Is it possible to override one or more of those settings using command line arguments. For example, if I wanted to specify that no preemptible machines should be used, can I do the following:
nextflow run main.nf -c nextflow.config --google.lifeSciences.preemptible false
?
Overriding pipeline parameters can be done using Nextflow's command line interface by prefixing the parameter name with a double dash. For example, put the following in a file called 'test.nf':
#!/usr/bin/env nextflow
params.greeting = 'Hello'
names = Channel.of( "foo", "bar", "baz" )
process greet {
input:
val name from names
output:
stdout result
"""
echo "${params.greeting} ${name}"
"""
}
result.view { it.trim() }
And run it using:
nextflow run -ansi-log false test.nf --greeting 'Bonjour'
Results:
N E X T F L O W ~ version 20.10.0
Launching `test.nf` [backstabbing_cajal] - revision: 431ef92cef
[46/22b4f0] Submitted process > greet (1)
[ca/32992c] Submitted process > greet (3)
[6e/5880b0] Submitted process > greet (2)
Bonjour bar
Bonjour foo
Bonjour baz
This works fine for pipeline params, but AFAIK there's no way to directly override executor config like you describe on the command line. You can however, just parameterize these values and set them on the command line like described above. For example, in your nextflow.config:
params {
gc_region = false
gc_preemptible = true
...
}
profiles {
'test' {
includeConfig 'conf/test.config'
}
'google' {
includeConfig 'conf/google.config'
}
...
}
And in a file called 'conf/google.config':
google {
project = "cool-project"
region = params.gc_region
lifeSciences {
bootDiskSize = "200 GB"
debug = true
preemptible = params.gc_preemptible
}
}
Then you should be able to override these in the usual way:
nextflow run main.nf -profile google --gc_region "europe-west4" --gc_preemptible false
Note that you can also specify multiple configuration profiles by separating the profile names with a comma:
nextflow run main.nf -profile google,test ...

channel checks as empty even if it has content

I am trying to have a process that is launched only if a combination of conditions is met, but when checking if a channel has a path to a file, it always returns it as empty. Probably I am doing something wrong, in that case please correct my code. I tried to follow some of the suggestions in this issue but no success.
Consider the following minimal example:
process one {
output:
file("test.txt") into _chProcessTwo
script:
"""
echo "Hello world" > "test.txt"
"""
}
// making a copy so I check first if something in the channel or not
// avoids raising exception of MultipleInputChannel
_chProcessTwo.into{
_chProcessTwoView;
_chProcessTwoCheck;
_chProcessTwoUse
}
//print contents of channel
println "Channel contents: " + _chProcessTwoView.toList().view()
process two {
input:
file(myInput) from _chProcessTwoUse
when:
(!_chProcessTwoCheck.toList().isEmpty())
script:
def test = _chProcessTwoUse.toList().isEmpty() ? "I'm empty" : "I'm NOT empty"
println "The outcome is: " + test
}
I want to have process two run if and only if there is a file in the _chProcessTwo channel.
If I run the above code I obtain:
marius#dev:~/pipeline$ ./bin/nextflow run test.nf
N E X T F L O W ~ version 19.09.0-edge
Launching `test.nf` [infallible_gutenberg] - revision: 9f57464dc1
[c8/bf38f5] process > one [100%] 1 of 1 ✔
[- ] process > two -
[/home/marius/pipeline/work/c8/bf38f595d759686a497bb4a49e9778/test.txt]
where the last line are actually the contents of _chProcessTwoView
If I remove the when directive from the second process I get:
marius#mg-dev:~/pipeline$ ./bin/nextflow run test.nf
N E X T F L O W ~ version 19.09.0-edge
Launching `test.nf` [modest_descartes] - revision: 5b2bbfea6a
[57/1b7b97] process > one [100%] 1 of 1 ✔
[a9/e4b82d] process > two [100%] 1 of 1 ✔
[/home/marius/pipeline/work/57/1b7b979933ca9e936a3c0bb640c37e/test.txt]
with the contents of the second worker .command.log file being: The outcome is: I'm empty
I tried also without toList()
What am I doing wrong? Thank you in advance
Update: a workaround would be to check _chProcessTwoUse.view() != "" but that is pretty dirty
Update 2 as required by #Steve, I've updated the code to reflect a bit more the actual conditions i have in my own pipeline:
def runProcessOne = true
process one {
when:
runProcessOne
output:
file("inputProcessTwo.txt") into _chProcessTwo optional true
file("inputProcessThree.txt") into _chProcessThree optional true
script:
// this would replace the probability that output is not created
def outputSomething = false
"""
if ${outputSomething}; then
echo "Hello world" > "inputProcessTwo.txt"
echo "Goodbye world" > "inputProcessThree.txt"
else
echo "Sorry. Process one did not write to file."
fi
"""
}
// making a copy so I check first if something in the channel or not
// avoids raising exception of MultipleInputChannel
_chProcessTwo.into{
_chProcessTwoView;
_chProcessTwoCheck;
_chProcessTwoUse
}
//print contents of channel
println "Channel contents: " + _chProcessTwoView.view()
println _chProcessTwoView.view() ? "Me empty" : "NOT empty"
process two {
input:
file(myInput) from _chProcessTwoUse
when:
(runProcessOne)
script:
"""
echo "The outcome is: ${myInput}"
"""
}
process three {
input:
file(defaultInput) from _chUpstreamProcesses
file(inputFromProcessTwo) from _chProcessThree
script:
def extra_parameters = _chProcessThree.isEmpty() ? "" : "--extra-input " + inputFromProcessTwo
"""
echo "Hooray! We got: ${extra_parameters}"
"""
}
As #Steve mentioned, I should not even check if a channel is empty, NextFlow should know better to not initiate the process. But I think in this construct I will have to.
Marius
I think part of the problem here is that process 'one' creates only optional outputs. This makes dealing with the optional inputs in process 'three' a bit tricky. I would try to reconcile this if possible. If this can't be reconciled, then you'll need to deal with the optional inputs in process 'three'. To do this, you'll basically need to create a dummy file, pass it into the channel using the ifEmpty operator, then use the name of the dummy file to check whether or not to prepend the argument's prefix. It's a bit of a hack, but it works pretty well.
The first step is to actually create the dummy file. I like shareable pipelines, so I would just create this in your baseDir, perhaps under a folder called 'assets':
mkdir assets
touch assets/NO_FILE
Then pass in your dummy file if your '_chProcessThree' channel is empty:
params.dummy_file = "${baseDir}/assets/NO_FILE"
dummy_file = file(params.dummy_file)
process three {
input:
file(defaultInput) from _chUpstreamProcesses
file(optfile) from _chProcessThree.ifEmpty(dummy_file)
script:
def extra_parameters = optfile.name != 'NO_FILE' ? "--extra-input ${optfile}" : ''
"""
echo "Hooray! We got: ${extra_parameters}"
"""
}
Also, these lines are problematic:
//print contents of channel
println "Channel contents: " + _chProcessTwoView.view()
println _chProcessTwoView.view() ? "Me empty" : "NOT empty"
Calling view() will emit all values from the channel to stdout. You can ignore whatever value it returns. Unless you enable DSL2, the channel will then be empty. I think what you're looking for here is a closure:
_chProcessTwoView.view { "Found: $it" }
Be sure to append -ansi-log false to your nextflow run command so the output doesn't get clobbered. HTH.

How to use conditions in .gitlab-ci.yml variables?

I want to know, if it's possible to set custom Gitlab CI variable from if-else condition statement.
In my .gitlab-ci.yml file I have the following:
variables:
PROJECT_VERSION: (if [ "${CI_COMMIT_TAG}" == "" ]; then "${CI_COMMIT_REF_NAME}-${CI_PIPELINE_ID}"; else ${CI_COMMIT_TAG}; fi);
Trying to set project version:
image: php:7.1-cli
stage: test
script:
# this echoes correct string (eg. "master-2794")
- (if [ "${CI_COMMIT_TAG}" == "" ]; then echo "${CI_COMMIT_REF_NAME}-${CI_PIPELINE_ID}"; else echo ${CI_COMMIT_TAG}; fi);
# this echoes something like "(if [ "" == "" ]; then "master-2794"; else ; fi);"
- echo $PROJECT_VERSION
Can this be done? If so, what have I missed? Thanks
This is expected behavior.
CI_COMMIT_TAG is only set to a value in a GitLab job. From https://docs.gitlab.com/ee/ci/variables/README.html
CI_COMMIT_TAG - The commit tag name. Present only when building tags.
Therefore in the variables section CI_COMMIT_TAG is not defined, hence equals to "".
So if you want to use CI_COMMIT_TAG use in job where tags are defined. See https://docs.gitlab.com/ee/ci/yaml/README.html#tags
It is possible:
Add your logic into the variable section:
variables:
VERSION_LOGIC: '(if [ "$${CI_COMMIT_TAG}" == "" ]; then echo "1.3.5.$$CI_PIPELINE_IID"; else echo "$${CI_COMMIT_TAG}"; fi);'
Now you are able to use this logic in a script secion of a job:
version:
stage: versioning
script:
- VERSION=$(eval $VERSION_LOGIC)
- echo "The current version is set to ${VERSION}."