Is your feature request related to a problem? Please describe

Describe the solution you'd like

Describe alternatives you've considered

Additional context

Think if there is a better way of including what the pipeline does in the check_replicates process for the DSL2 pipeline

as the titel says, the samplesheets for full size tests should be stored in nf-core/test-datasets. If we ever need to move data then releases won't be affected and break

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/dualrnaseq pipeline documentation

Description of the bug

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line:
2. See error:

Expected behaviour

Log files

Have you provided the following extra information/files:

• The command used to run the pipeline
• The .nextflow.log file

System

• Hardware:
• Executor:
• OS:
• Version

Nextflow Installation

• Version:

Container engine

• Engine:
• version:
• Image tag:

Additional context

Please add the Zenodo DOI to the main README.md

[![DOI](https://zenodo.org/badge/309982089.svg)](https://zenodo.org/badge/latestdoi/309982089)

At some point, commits from dev have been merged into the TEMPLATE branch. This makes the TEMPLATE branch "dirty" and will make the automated template synchronisation pull requests super difficult to merge.

Docs on how to fix this are here: https://nf-co.re/developers/sync#fixing-a-broken-template-branch - please do in conversation with me / other core-team members on Slack though. If I find time I will try to sort this out myself in the coming days.

Description of the bug

I'm not sure if this is a bug or by design. There are parameters to override the default feature names in the host and pathogen annotations, but I'm not sure if they are being used in all parts of the pipeline. For instance, I get failures when running the step which calls extract_annotations_from_gff.py because it cannot find any features. When I look in the script I can see that 'gene_type', 'gene_id', 'gene_name', and 'transcript_name' are hardcoded, and thus the parameters which I specify to override these feature names are not used in this script. If I manually edit this file to use the corresponding feature names, it works.

Steps to reproduce

Use a reference annotation from Ensembl such as Saccharomyces_cerevisiae.R64-1-1.34.gff3 or Schizosaccharomyces_pombe.ASM294v2.51.gff3 which does not contain the default feature names.

Expected behaviour

I expect the feature names I specify when running the pipeline to override the default names, but the names in this script are hardcoded.

Currently, this pipeline will not run on the latest version of Nextflow. The error message " Nextflow DSL1 is no longer supported — Update your script to DSL2, or use Nextflow 22.10.x or earlier", appears.

This line doesn't seem to be parsing gff features correctly when more than one feature is given to the -gene_feature_gff_to_create_transcriptome_pathogen flag:

In my case, I'm getting the error "No features matched the input criteria of: ['genencRNARiboswitchthree_prime_utrfive_prime_utrIntron'] and locus_tag"

Possibly, the same applies to -gene_attribute_gff_to_create_transcriptome_pathogen and the respective host flags, but I didn't check those.

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Describe alternatives you've considered

Additional context

Describe the solution you'd like

Put test data from DSL1 implementation into the common and integrate it with the pipeline

nf-core/dualrnaseq feature request

Create the STAR_HTSEQ subworkflow + HTSEQ module as a part of moving this pipeline to the DSL2.

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Describe alternatives you've considered

Additional context

The pipeline is now getting a bit behind the nf-core template. It needs to be updated before any further development work can be done on the pipeline.

First, the TEMPLATE branch needs to be fixed - #13

Then a new automated sync PR needs to be created, as fixing #13 will remove the commits in #12 (closing new preemptively).

Again, I will try to have a go at fixing this stuff up myself in the coming days. At least opening the PR anyway, I will see about resolving the merge conflicts. If they're not too bad then I will try.

convert the create_transcriptome_fasta_pathogen process into a module and add it to the pipeline

nf-core/dualrnaseq feature request

Migrate salmon index and salmon quantification from DSL1 to DSL2.

Is your feature request related to a problem? Please describe

Dual RNA-seq pipeline uses DSL1. As a part of DSL2 migration effort salmon index and quantification must be migrated to DSL2.

Describe the solution you'd like

Salmon index and quantification are already publicly available nf-core modules. These were integrated to the pipeline.

Describe alternatives you've considered

Since there are nf-core salmon modules, there are not better solutions than to integrate them to the pipeline.

Additional context

Is your feature request related to a problem? Please describe

As part of translating the pipeline from DSL to DSL2, the process needs to be converted to DSL2.

Describe the solution you'd like

Re-writing the process and including the bin/split_quant_tables_salmon.sh script within the process definition.

Describe alternatives you've considered

Additional context

https://github.com/nf-core/dualrnaseq/blob/master/bin/split_quant_tables_salmon.sh

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Describe alternatives you've considered

Additional context

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Describe alternatives you've considered

Additional context

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/dualrnaseq pipeline documentation

Description of the bug

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line:
2. See error:

Expected behaviour

Log files

Have you provided the following extra information/files:

• The command used to run the pipeline
• The .nextflow.log file

System

• Hardware:
• Executor:
• OS:
• Version

Nextflow Installation

• Version:

Container engine

• Engine:
• version:
• Image tag:

Additional context

Is your feature request related to a problem? Please describe

Describe the solution you'd like

This is about creating common module that will use /bin/collect_quantification_data.py and possibly replace following modules

• combine_quantification_tables_salmon
• combine_host_quant_gene_level_salmon
• combine_annotations_quant_gene_level_salmon
• combine_host_quant_gene_level_salmon_alignment
• combine_quantification_tables_salmon_alignment_mode

Describe alternatives you've considered

Additional context

Pretty much as the title says. The current output when setting --outWigType is a unique coverage file for the merged host-pathogen genome. This is not ideal for visualization, therefore getting separate files would be of great help.

In the replace_attribute_host_genome_gff_star_salmon process "Parent" is hard-coded, it should be a use-defined parameter $host_attribute

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Describe alternatives you've considered

Additional context

Is your feature request related to a problem? Please describe

Seaborn v11.2 has totally dropped the JointGrid.annotate() method after previous version threw warnings saying it would be deprecated which causes an issue with the scatter_plots.py script in the bin directory.

Describe the solution you'd like

A way of inserting the Pearson's R value text into the top left corner of the scatterplots that also works on Seaborn v.0.11.2 and also on legacy v0.9.0.

Describe alternatives you've considered

Use Matplotlib's Axes text() feature, which Seaborn allows, though a simple top left positioning requires some "chewing" and Pearson's r has to be precalculated because this method does not accept a function, and has no convenient positioning via loc as annotate() used to.

The following could possibly do it (at line 35 bin/scatter_plots.py)

    pearr = stats.pearsonr(TPMs.rep1,TPMs.rep2)
    st=f"Pearson's r = {pearr[0]:.4f}"
    g1.ax_joint.text(0.05, 0.95, st, fontsize=15, transform=g1.ax_joint.transAxes, verticalalignment='top')

Additional context

Proof of concept:

#!/usr/bin/env python3
# This works for both Seaborn v0.9.0 and v0.11.2
import seaborn as sns
from scipy import stats
import matplotlib.pyplot as plt

tips = sns.load_dataset("tips")

g = sns.JointGrid(x="total_bill", y="tip", data=tips)
g = g.plot_joint(plt.scatter, color="g", s=40, edgecolor="white")
g = g.plot_marginals(sns.distplot, kde=False, color="g")

# OK here is the deprecated annotate function, This will only work in v0.9.0 with deprecation warning.
# g = g.annotate(stats.pearsonr, template="{stat}: {val:.4f}", stat="Pearson's r", loc="upper left", fontsize=15)
# alternative requires a few more lines:
pearr= stats.pearsonr(tips.total_bill, tips.tip) # precalc
st=f"Pearson's r = {pearr[0]:.4f}" # stringify
g.ax_joint.text(0.05, 0.95, st, fontsize=15, transform=g.ax_joint.transAxes, verticalalignment='top')
g.savefig("d09.pdf", format="pdf")

nf-core/dualrnaseq feature request

Create a new module to combine the host ambig and unique counts.

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Move host_comb_ambig_uniq_alignment_based process as a separate nf-core module (DSL1 --> DSL2).

Describe alternatives you've considered

Additional context

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Describe alternatives you've considered

Additional context

nf-core/dualrnaseq feature request

Hi there!

Is your feature request related to a problem? Please describe

As part of translating the pipeline from DSL to DSL2, the process Cutadapt needs to be converted to DSL2.

Describe the solution you'd like

Using code from nf-core Modules repository

Describe alternatives you've considered

Additional context

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/dualrnaseq pipeline documentation

Description of the bug

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line:
2. See error:

Log files

Jul-20 15:28:18.394 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/dualrnaseq -r 1.0.0 -profile docker --input '/mnt/f/tes/.fastq.gz' --single_end = true --fasta_host /mnt/c/Linux/references/GRCh38_latest.fa --fasta_pathogen /mnt/c/Linux/references/NC_045512_2.fasta --gff_host /mnt/c/Linux/references/GRCh38_latest_genomic.gff --gff_pathogen /mnt/c/Linux/references/NC_045512_2_genomic.gff --run_star --outdir /mnt/c/Linux/tesr
Jul-20 15:28:18.474 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 21.04.2
Jul-20 15:28:19.193 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/rui/.nextflow/assets/nf-core/dualrnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/dualrnaseq.git
Jul-20 15:28:19.211 [main] DEBUG nextflow.scm.AssetManager - Git config: /home/rui/.nextflow/assets/nf-core/dualrnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/dualrnaseq.git
Jul-20 15:28:19.346 [main] INFO nextflow.cli.CmdRun - Launching nf-core/dualrnaseq [voluminous_lovelace] - revision: d8dcd8a [1.0.0]
Jul-20 15:28:19.761 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /home/rui/.nextflow/assets/nf-core/dualrnaseq/nextflow.config
Jul-20 15:28:19.762 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home/rui/.nextflow/assets/nf-core/dualrnaseq/nextflow.config
Jul-20 15:28:19.768 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: docker
Jul-20 15:28:19.979 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jul-20 15:28:19.980 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jul-20 15:28:19.983 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Jul-20 15:28:20.143 [main] DEBUG nextflow.config.ConfigBuilder - In the following config snippet the attribute params.genomes_ignore is empty:
genome_host=false
genome_pathogen=false
input='/mnt/f/tes/.fastq.gz'
single_end='='
outdir='/mnt/c/Linux/tesr'
publish_dir_mode='copy'
run_cutadapt=false
a='AGATCGGAAGAGCACACGTCTGAACTCCAGTCA'
A='AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT'
quality_cutoff='10'
cutadapt_params=''
run_bbduk=false
minlen='18'
qtrim='r'
trimq='10'
ktrim='r'
k='17'
mink='11'
hdist='1'
adapters=/home/rui/.nextflow/assets/nf-core/dualrnaseq/assets/adapters.fa
bbduk_params=''
skip_fastqc=false
fastqc_params=''
libtype=''
generate_salmon_uniq_ambig=false
incompatPrior=0.0
gene_attribute_gff_to_create_transcriptome_host='transcript_id'
gene_feature_gff_to_create_transcriptome_host=['exon', 'tRNA']
gene_attribute_gff_to_create_transcriptome_pathogen='locus_tag'
gene_feature_gff_to_create_transcriptome_pathogen=['gene', 'sRNA', 'tRNA', 'rRNA']
read_transcriptome_fasta_host_from_file=false
read_transcriptome_fasta_pathogen_from_file=false
run_salmon_selective_alignment=false
kmer_length=21
writeUnmappedNames=false
softclipOverhangs=false
dumpEq=false
writeMappings=false
keepDuplicates=false
salmon_sa_params_index=''
salmon_sa_params_mapping=''
run_star=true
outSAMunmapped='Within'
outSAMattributes='Standard'
outFilterMultimapNmax=999
outFilterType='BySJout'
alignSJoverhangMin=8
alignSJDBoverhangMin=1
outFilterMismatchNmax=999
outFilterMismatchNoverReadLmax=1
alignIntronMin=20
alignIntronMax=1000000
alignMatesGapMax=1000000
limitBAMsortRAM=0
winAnchorMultimapNmax=999
sjdbOverhang=100
outWigType='None'
outWigStrand='Stranded'
star_index_params=''
star_alignment_params=''
quantTranscriptomeBan='Singleend'
star_salmon_index_params=''
star_salmon_alignment_params=''
run_salmon_alignment_based_mode=false
salmon_alignment_based_params=''
run_htseq_uniquely_mapped=false
stranded='yes'
max_reads_in_buffer=30000000
minaqual=10
gene_feature_gff_to_quantify_host=['exon', 'tRNA']
gene_feature_gff_to_quantify_pathogen=['gene', 'sRNA', 'tRNA', 'rRNA']
host_gff_attribute='gene_id'
pathogen_gff_attribute='locus_tag'
htseq_params=''
mapping_statistics=false
rna_classes_to_replace_host=/home/rui/.nextflow/assets/nf-core/dualrnaseq/data/RNA_classes_to_replace.tsv
custom_config_version='master'
fasta_host='/mnt/c/Linux/references/GRCh38_latest.fa'
fasta_pathogen='/mnt/c/Linux/references/NC_045512_2.fasta'
gff_host='/mnt/c/Linux/references/GRCh38_latest_genomic.gff'
gff_pathogen='/mnt/c/Linux/references/NC_045512_2_genomic.gff'
custom_config_base=https://raw.githubusercontent.com/nf-core/configs/master
hostnames=['binac':['.binac.uni-tuebingen.de'], 'cbe':['.cbe.vbc.ac.at'], 'cfc':['.hpc.uni-tuebingen.de'], 'crick':['.thecrick.org'], 'icr_davros':['.davros.compute.estate'], 'imperial':['.hpc.ic.ac.uk'], 'imperial_mb':['.hpc.ic.ac.uk'], 'genotoul':['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], 'genouest':['.genouest.org'], 'uppmax':['.uppmax.uu.se'], 'utd_ganymede':['ganymede.utdallas.edu'], 'utd_sysbio':['sysbio.utdallas.edu']]
config_profile_description=false
config_profile_contact=false
config_profile_url=false
name=false
multiqc_config=false
email=false
email_on_fail=false
max_multiqc_email_size=25 MB
plaintext_email=false
monochrome_logs=false
help=false
tracedir=/mnt/c/Linux/tesr/pipeline_info
max_memory=128 GB
max_cpus=16
max_time=10d
genomes {
GRCh38 {
fasta_host='path_to_references/human/GRCh38.genome.fa'
gff_host='path_to_references/human/GRCh38.annotation.gff3'
gff_host_tRNA='path_to_references/human/GRCh38.gencode.tRNAs.gff3'
transcriptome_host='path_to_references/human/GRCh38.gencode.transcripts.fa'
}
SL1344 {
fasta_pathogen='path_to_references/Salmonella/SL1344.fasta'
gff_pathogen='path_to_references/Salmonella/SL1344.gff'
}
My_Bacteria {
fasta_pathogen='path_to_references/My_Bacteria/My_Bacteria.fasta'
gff_pathogen='path_to_references/My_Bacteria/My_Bacteria.gff'
}
}

Jul-20 15:28:20.147 [main] ERROR nextflow.cli.Launcher - Unknown config attribute params.genomes_ignore -- check config file: /home/rui/.nextflow/assets/nf-core/dualrnaseq/nextflow.config
nextflow.exception.ConfigParseException: Unknown config attribute params.genomes_ignore -- check config file: /home/rui/.nextflow/assets/nf-core/dualrnaseq/nextflow.config
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:72)
at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrapNoCoerce.callConstructor(ConstructorSite.java:105)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:59)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:263)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:277)
at nextflow.config.ConfigBuilder.validate(ConfigBuilder.groovy:444)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:193)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:61)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:212)
at nextflow.config.ConfigBuilder.validate(ConfigBuilder.groovy:451)
at nextflow.config.ConfigBuilder.validate(ConfigBuilder.groovy:431)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:193)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:61)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:194)
at nextflow.config.ConfigBuilder.merge0(ConfigBuilder.groovy:405)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:193)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:61)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:203)
at nextflow.config.ConfigBuilder.buildConfig0(ConfigBuilder.groovy:354)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:193)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:61)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:194)
at nextflow.config.ConfigBuilder.buildGivenFiles(ConfigBuilder.groovy:312)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:193)
at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:61)
at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:171)
at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:185)
at nextflow.config.ConfigBuilder.buildConfigObject(ConfigBuilder.groovy:729)
at nextflow.config.ConfigBuilder.build(ConfigBuilder.groovy:742)
at nextflow.cli.CmdRun.run(CmdRun.groovy:272)
at nextflow.cli.Launcher.run(Launcher.groovy:475)
at nextflow.cli.Launcher.main(Launcher.groovy:657)

System

• Hardware:
• Executor:
• OS:
• Version

Nextflow Installation

• Version:

Container engine

• Engine:
• version:
• Image tag:

Additional context

Is your feature request related to a problem? Please describe

Describe the solution you'd like

Describe alternatives you've considered

Additional context

nf-core/dualrnaseq feature request

Update extract_annotations to DSL2

Is your feature request related to a problem? Please describe

As part of translating the pipeline from DSL1 to DSL2, the processes family extract_annotations_* needs to be converted to DSL2.

Describe the solution you'd like

Create a new module for that

Describe alternatives you've considered

Additional context