ch_results
        .combine(inputs.filter_params, by:0)
        .view()

ch_results
        .combine(inputs.filter_params)
        .map { meta1, file, meta2, filter_params ->
            if (meta1 == meta2) {
                return [meta2, file, filter_params]
            }
        }
        .view()

ext.args

params

ext.args

output

ERROR ~ Error executing process > 'NFCORE_METABOIGNITER:METABOIGNITER:ANNOTATION_REQ:OPENMS_METABOLITEADDUCTDECHARGER (42-r001)'

Caused by:
  Process `NFCORE_METABOIGNITER:METABOIGNITER:ANNOTATION_REQ:OPENMS_METABOLITEADDUCTDECHARGER (42-r001)` terminated with an error exit status (8)


Command executed:

  mkdir output
  
  MetaboliteAdductDecharger \
                      -in 42-r001.merged.featureXML -out_fm output/42-r001.featureXML -algorithm:MetaboliteFeatureDeconvolution:potential_adducts H-1:-1:0.6 CH3COO:-1:0.4 -algorithm:MetaboliteFeatureDeconvolution:charge_min 1 -algorithm:MetaboliteFeatureDeconvolution:charge_max 2 -algorithm:MetaboliteFeatureDeconvolution:charge_span_max 1 -algorithm:MetaboliteFeatureDeconvolution:q_try heuristic -algorithm:MetaboliteFeatureDeconvolution:retention_max_diff 2.5 -algorithm:MetaboliteFeatureDeconvolution:retention_max_diff_local 2.0 -algorithm:MetaboliteFeatureDeconvolution:mass_max_diff 10 -algorithm:MetaboliteFeatureDeconvolution:unit ppm -algorithm:MetaboliteFeatureDeconvolution:max_neutrals 1 -algorithm:MetaboliteFeatureDeconvolution:use_minority_bound true -algorithm:MetaboliteFeatureDeconvolution:max_minority_bound 1 -algorithm:MetaboliteFeatureDeconvolution:min_rt_overlap 0.66 -algorithm:MetaboliteFeatureDeconvolution:intensity_filter -algorithm:MetaboliteFeatureDeconvolution:negative_mode -algorithm:MetaboliteFeatureDeconvolution:default_map_label 'decharged features'
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_METABOIGNITER:METABOIGNITER:ANNOTATION_REQ:OPENMS_METABOLITEADDUCTDECHARGER":
      openms: $(OpenMSInfo | awk '/OpenMS Version/{getline; getline; print $3}')
  END_VERSIONS

Command exit status:
  8

Command output:
  Parameters 'retention_max_diff' and 'retention_max_diff_local' are unequal, but no RT shift of adducts has been defined. Setting parameters to minimum of the two.
  MassExplainer table size: 2
  Generating Masses with threshold: -1.42712 ...
  done

Command error:
  Parameters 'retention_max_diff' and 'retention_max_diff_local' are unequal, but no RT shift of adducts has been defined. Setting parameters to minimum of the two.
  MassExplainer table size: 2
  Generating Masses with threshold: -1.42712 ...
  done
  Error: Unexpected internal error (WARNING!!! implicit number of default adduct is negative!!! left:-2 right: -2
  )

Work dir:
  /home/plashmore/projects/gitlab/naca-smoke-taint/03-metaboigniter/work/5b/4095405550b2dd572032ba76fd2a20

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details
ERROR ~ Failed to invoke `workflow.onComplete` event handler

 -- Check script '/home/plashmore/.nextflow/assets/nf-core/metaboigniter/./workflows/../subworkflows/local/utils_nfcore_metaboigniter_pipeline/main.nf' at line: 123 or see '.nextflow.log' file for more details

thread_ch = channel.of(params.threads)
    ref_ch = channel.fromPath(params.ref)
        .map { it.toString() }
    fq_ch = channel.fromPath(params.fq)
        .map { it.toString() }
    saw_ch = channel.fromPath(params.saw_path)
        .map { it.toString() }

    cleanreads_list = saw_ch.concat( id_ch, whitelist_ch.flatten(), fq_ch, ref_ch, thread_ch )
        .collect()
    //    .view()
    cleanreads_ch = Channel.fromList( cleanreads_list ).view()

<http://STRS_mategenomics_1.nf|STRS_mategenomics_1.nf>

channel.fromList

concat

process XX { conda.enabled=false;... }

.github/snapshots/

!

withName: '!PROC1|PROC2|PROC3' {
        container = null
    }

withName: '!(PROC1|PROC2|PROC3)' {
        container = null
    }

<http://log.info|log.info> "About to run squares"
    nums = Channel.of(1, 2, 3, 4) 
    square = nums.map { it -> it * it } 
    square.view()
    <http://log.info|log.info> "Successfully ran squares"

About to run squares
Successfully ran squares

\033[0;35m  nf-core/bactiseq ${manifest.version}\033[0m

path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },

nf-core <pipelinename> -profile test,docker --outdir results

def getRegionFromFai(input_region, ch_fasta) {
    def ch_regions = Channel.empty()
    // ch_fasta.view()
    // Gather regions to use and create the meta map
    if (input_region ==~ '^(chr)?[0-9XYM]+$' || input_region == "all") {
        ch_regions = ch_fasta.map{ it -> it[2] }
            .splitCsv(header: ["chr", "size", "offset", "lidebase", "linewidth", "qualoffset"], sep: "\t")
            .map{it -> [chr:it.chr, region:"0-"+it.size]}
        if (input_region != "all") {
            ch_regions = ch_regions.filter{it.chr == input_region}
        }
        ch_regions = ch_regions
            .map{ [[chr: it.chr, region: it.chr + ":" + it.region], it.chr + ":" + it.region]}
    } else {
        if (input_region ==~ '^chr[0-9XYM]+:[0-9]+-[0-9]+$') {
            ch_regions = Channel.from([input_region])
                .map{ [[chr: it.split(":")[0], "region": it], it]}
        } else {
            error "Invalid input_region: ${input_region}"
        }
    }
    return ch_regions
}

java.lang.IndexOutOfBoundsException: toIndex = 3

function.result

process {
  resourceLimits = [
    cpus: 48,
    memory: 450.GB,
    time: 120.h
  ]
}

nextflow -bg -c maxresourceLimits.config run nf-core/funcscan my_command

nextflow -bg -C maxresourceLimits.config run nf-core/funcscan my_command

nf-core modules install gfatools/gfa2fa


                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.3.1 - <https://nf-co.re>


ERROR    tuple index out of range

nextflow run nf-core/rnaseq -profile test,conda --outdir rna_results_06_22v3

[-        ] NFCORE_RNASEQ:RNASEQ:MULTIQC                                                               -
Creating env using conda: /home/pmendez00/.nextflow/assets/nf-core/rnaseq/modules/nf-core/trimgalore/environment.yml [cache /home/pmendez00/.conda/nfcore_cache/env-3cb1f98716d46bb0-7ee73282f0ad4cb3bfb895355fb91bd7]
Creating env using conda: /home/pmendez00/.nextflow/assets/nf-core/rnaseq/modules/nf-core/fq/lint/environment.yml [cache /home/pmendez00/.conda/nfcore_cache/env-930a3c51c1f4168e-16bfc74f50473b17f7bf05d44dde0205]
Creating env using conda: /home/pmendez00/.nextflow/assets/nf-core/rnaseq/modules/nf-core/fastqc/environment.yml [cache /home/pmendez00/.conda/nfcore_cache/env-44672b7451831d70-3ea42529974ca5a54ae5623eacfbc76a]
Creating env using conda: /home/pmendez00/.nextflow/assets/nf-core/rnaseq/modules/nf-core/untar/environment.yml [cache /home/pmendez00/.conda/nfcore_cache/env-6336a1b7bbcc0c23-cac18ad63488da9f5109ab1f794a29f6]
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/rnaseq] Pipeline completed with errors-
Creating env using conda: /home/pmendez00/.nextflow/assets/nf-core/rnaseq/modules/nf-core/cat/fastq/environment.yml [cache /home/pmendez00/.conda/nfcore_cache/env-dc4947c2aa26d50f-809d7bbc0708e58c59ba558c02e39e97]
WARN: Directive `process.shell` cannot contain new-line characters - offending value: [bash

set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
]
ERROR ~ Error executing process > 'NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)'

Caused by:
  Process `NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)` terminated with an error exit status (126)


Command executed:

  # Not calling gunzip itself because it creates files
  # with the original group ownership rather than the
  # default one for that user / the work directory
  gzip \
      -cd \
       \
      gfp.fa.gz \
      > gfp.fa
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA":
      gunzip: $(echo $(gunzip --version 2>&1) | sed 's/^.*(gzip) //; s/ Copyright.*$//')
  END_VERSIONS

Command exit status:
  126

Command output:
  (empty)

Command error:
  .command.run: line 299: .command.run: Permission denied

Work dir:
  /home/pmendez00/nfcore_runs/work/34/d295729ecc2cd244e2683cc5195745

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: <https://nf-co.re/docs/usage/troubleshooting>

 -- Check '.nextflow.log' file for details

.command.sh: line 9: sampleA.read_distribution.txt: cannot overwrite existing file

read_distribution.py \
      -i sampleA.dedup.bam \
      -r GRCh38_gencode_v22_CTAT_lib_Mar012021.ref_annot.gtf.bed \
      > sampleA.read_distribution.txt

nextflow run <http://main.nf|main.nf> -profile apptainer  --input=testSampleSheet.csv

FROM continuumio/miniconda3

# Copy environment YAML files into the image
COPY assets/kneaddata.yaml .
COPY assets/metaphlan.yaml .
COPY assets/humann.yaml .
COPY assets/analysis_r.yaml .
COPY assets/cp_r.yaml .

# Create the conda environments
RUN conda env create -f kneaddata.yaml
RUN conda env create -f metaphlan.yaml
RUN conda env create -f humann.yaml
RUN conda env create -f analysis_r.yaml
RUN conda env create -f cp_r.yaml

# List all environments to verify
RUN conda env list

# Copy R script into the image
COPY bin/analysis.R /bin/analysis.R
COPY bin/cp.R /bin/cp.R

# Set default shell to base env
CMD ["bash"]

TEMPLATE

dev

TEMPLATE

TEMPLATE

# Delete branch locally
git branch -D TEMPLATE
# Create a new orphan TEMPLATE branch
git checkout --orphan TEMPLATE
# Removing all files
git rm -r .
# Create a new TEMPLATE branch without affecting other branches of my pipeline
nf-core pipelines create --no-git
# Pushing this branch
git add .
git commit -m "Reset TEMPLATE branch with clean nf-core template"
git push origin TEMPLATE --force

nf-core pipelines create

TEMPLATE