Bulut Hamali
05/07/2024, 2:51 PMNisha Boora
05/08/2024, 7:50 AMnf-core create
template and nf-core modules, but I'm getting the following error:Oskar Wacker
05/08/2024, 9:13 AMJSONDecodeError
in the nf-core linting of my PR: https://github.com/nf-core/differentialabundance/actions/runs/8999075722/job/24720863161?pr=256
I had this error previously in another PR but it vanished when I fixed some missing square brackets in the Changelog (no idea how those would break the linting though). Does someone know what causes this error and how to solve it?lilin
05/08/2024, 10:44 AMArnelyn Larano
05/08/2024, 11:25 AMmvforster
05/08/2024, 2:03 PMRamiro Barrantes Reynolds
05/08/2024, 3:06 PMRyan Neilson
05/08/2024, 3:30 PMAMMAR SABIR
05/08/2024, 8:07 PMMarie Wong
05/09/2024, 1:41 AMNINO PARAMBALOTH LEENUS
05/10/2024, 6:04 AMyemi_codes
05/10/2024, 7:15 AMworkflow {
SAMPLESHEET(fastq_file_sorted_list_ch, prefix)
samplesheetToList(SAMPLESHEET.out, "assets/schema_input.json")
}
Here is the error:
N E X T F L O W ~ version 23.10.1
`Launching <http://main.nf|main.nf>
[suspicious_ramanujan] DSL2 - revision: e43df56770`
*Missing process or function samplesheetToList([DataflowVariable(value=null), assets/schema_input.json])* -- Did you mean 'samplesheetToList' instead?
Please help with solving this problem. The goal is to make sure I can use samplesheetToList function at runtime (without having to have already generated sample_sheet.csv fileArnelyn Larano
05/10/2024, 7:55 AMArnelyn Larano
05/10/2024, 7:57 AMVictor Kalbskopf
05/10/2024, 9:11 AMdownload.file(url, destfile)
command in R, it works fine.
url = "<ftp://victor:victorisgreat@127.0.0.1:2121/genes2exclude.txt>"
download.file(url, destfile = "genes2exclude.txt")
When the script is running part of an nf-core pipeline, I get:
Command error:
trying URL '<ftp://victor:victorisgreat@127.0.0.1:2121/genes2exclude.txt>'
Error in download.file(url, destfile = "genes2exclude.txt") :
cannot open URL '<ftp://victor:victorisgreat@127.0.0.1:2121/genes2exclude.txt>'
The test run and the nf-core pipeline are running on the same machine, and fetching it from localhost.AMMAR SABIR
05/10/2024, 4:00 PM"rmarkdown::render('read_count.R')" ${count_file_1}
, the same read_count.R is executed without rmarkdown::render i.e as "read_count.R"
in script block. Do you have any idea why it is not working ?Ramiro Barrantes Reynolds
05/10/2024, 8:24 PMprocess IDENTIFY_UMI {
publishDir "${params.outdir}/demux", mode: 'copy'
container '<docker://brianyee/umi_tools:1.0.0>'
input:
tuple val(sampleID), path(fasta)
output:
path "*.fq", emit: fastq
path "${sampleID}.UMI.R1.metrics"
script:
"""
umi_tools extract --random-seed 1 --bc-pattern NNNNNNNNNN --stdin ${fasta} --stdout ${sampleID}.UMI.R1\
.fq --log ${sampleID}.UMI.R1.metrics
"""
}
Arnelyn Larano
05/11/2024, 4:31 AMRamiro Barrantes Reynolds
05/11/2024, 11:36 PMSAMPLE,ID,TYPE,FASTQ1,FASTQ2
replicate1_signal,replicate1,signal,test-dataset/test1_R1.fastq.gz,test-dataset/test1_R2.fastq.gz replicate1_background,replicate1,background,test-dataset/test2_R1.fastq.gz,test-dataset/test2_R2.fastq.gz
I modified the assets/schema_input.json accordingly:
{
"$schema": "<http://json-schema.org/draft-07/schema>",
"$id": "<https://raw.githubusercontent.com/nf-core/eclipseq/master/assets/schema_input.json>",
"title": "nf-core/eclipseq pipeline - params.input schema",
"description": "Schema for the file provided with params.input",
"type": "array",
"items": {
"type": "object",
"properties": {
"SAMPLE": {
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "Sample name must be provided and cannot contain spaces",
"meta": ["sample"]
},
"ID": {
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "ID indicating replicate or sample name",
"meta": ["id"]
},
"TYPE": {
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "signal or background",
"meta": ["type"]
},
"FASTQ1": {
"type": "string",
"format": "file-path",
"exists": true,
"pattern": "^\\S+\\.f(ast)?q\\.gz$",
"errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension \
'.fq.gz' or '.fastq.gz'"
},
"FASTQ2": {
"type": "string",
"format": "file-path",
"exists": true,
"pattern": "^\\S+\\.f(ast)?q\\.gz$",
"errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fast\
q.gz'"
}
},
"required": ["SAMPLE","ID","TYPE", "FASTQ1"]
}
}
But do I also need to modify ./subworkflows/local/utils_nfcore_eclipseq_pipeline/main.nf
??
I am also wondering about actually reading the data, would it be as easy as calling them in a process like this (${meta.ID}, ${meta.FASTQ1}, ${meta.FASTQ2})??:
TRIM_ADAPTERS(ch_samplesheet)
where
process TRIM_ADAPTERS {
publishDir "${params.outdir}/trimmed", mode: 'copy'
container '<docker://brianyee/cutadapt:1.14>'
input:
tuple val(meta)
output:
path "*.fq", emit: fastq
script:
def sampleID = "${meta.ID}"
def FASTQ1 = "${meta.FASTQ1}"
def FASTQ2 = "${meta.FASTQ2}"
"""
cutadapt -f fastq \
--match-read-wildcards \
--times 1 \
-e 0.1 \
-O 1 \
--quality-cutoff 6 \
-m 18 \
-a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC \
-g CTTCCGATCTACAAGTT \
-g CTTCCGATCTTGGTCCT \
-o ${sampleID}_R1.trimmed.fq \
-p ${sampleID}_R2.trimmed.fq \
${FASTQ1} ${FASTQ2}
"""
}
Thank you for your help!!Arnelyn Larano
05/12/2024, 4:01 AMAnabella Trigila
05/13/2024, 2:08 PMSanjeevnextflow
05/13/2024, 4:36 PMprocess file_create {
publishDir path: "/data1/users/nextflow/learn_nextflow/files_created/", mode: 'copy'
input:
val (temp_number)
output:
path("${temp_number}.txt")
script:
"""
echo "value is $temp_number" > $temp_number".txt"
"""
}
workflow {
numbers=Channel.of(1, 2, 3, 40, 50)
file_create(numbers).collectFile(name: 'sample.txt', newLine: true)
}
I see that the sample.txt file is generated in work folder under tmp names directory.
How do I capture or pass it to another process?Jiri Novotny
05/13/2024, 6:00 PMnf-core download
now works, but I am struggling with nextflow self-update
and nextflow run nf-core/sarek -profile test
which both hang. I was monitoring server traffic with iftop
and tcpflow
, but now there's nothing which is not whitelisted (at least I hope so). Before I tell sysadmin to try some sort of monitoring to figure it out, do you have some list of URLs that must be whitelisted in order for nextflow/nf-core pipelines to work? Or the hanging could be caused by something else? Nextflow is installed in a conda env. Thanks a lot!Pieter Moris
05/15/2024, 10:19 AMext.args
and proper syntax in modules.config
files: I've seen several different ways of specifying these additional args:
• [ list, of, items].join(' ').trim()
(used by eager)
• [ ' ', list, of, items].join(' ').trim()
i.e. with an empty space at the start of the list (used by sarek)
• { [ list, of, items].join(' ').trim() }
i.e. wrapped in a closure (used by rnaseq, supposedly mandatory according when referencing params.*
https://nf-co.re/docs/contributing/tutorials/adding_modules_to_pipelines)
• { params.extra_fastp_args ?: '' }
i.e. simple closure when only passing 1 item.
Any recommendations here? I assume that wrapping everything in a closure is the best practice, but I'm not sure about the empty first item.Anabella Trigila
05/15/2024, 12:39 PM.splitText()
. I am reading a samplesheet that contains a list of .txt files. I want to extract and process the text content of the txt files.
I am using the .fromSamplesheet
from nf-validation to get a channel. The channel it produces looks like this:
[DUMP: ch_chunks_out] [['chr':'chr22'], '<https://github.com/nf-core/test-datasets/raw/f0622133837c9494a965d6cd3957629d4c7415f0/data/panel/22/chr22_chunks_glimpse1.txt>']
However, I can't simply ch_chunks_out.splitText()
because ERROR ~ Object of class 'java.util.LinkedHashMap' does not support 'splitter' methods.
I do not get this error when the channel is an emission from a process and the files are local, such as:
[DUMP: GLIMPSE_CHUNK.out.chunk_chr] [[''chr':'chr21'], /workspace/work/82/75a99d682775b92f72d28e754eba7e/1000GP.s.norel_chr21_chunks_glimpse1.txt]
GLIMPSE_CHUNK.out.chunk_chr
.splitText()
.map { metamap, line ->
def fields = line.split("\t")
def startEnd = fields[2].split(':')[1].split('-')
[metamap, metamap.chr, startEnd[0], startEnd[1]]
}
What would be the best approach to modify ch_chunks_out
so that it works with .splitText()
? Thank you!Raunak Vijay
05/15/2024, 3:35 PMMariana Gonzales Andre
05/16/2024, 9:51 AMMurray Wham
05/16/2024, 3:52 PMexport MOSDEPTH_Q0=NO_COVERAGE
export MOSDEPTH_Q1=LOW_COVERAGE
export MOSDEPTH_Q2=CALLABLE
mosdepth -Q 1 --quantize 0:1:4: --by targets.bed some_prefix sample.bam
I can write a process for it (or use the nf-core one), and write a config for it:
process {
withName: MOSDEPTH {
beforeScript = "export MOSDEPTH_Q0=NO_COVERAGE; ...
}
}
But then if I want to use my institutional config file that sets beforeScript as well for singularity, Nextflow will only pick one depending on the order in which I specify config files, and I can't combine them. I've written my own mosdepth process for now, but wanted to know if anyone else has ever run into this?Kyle Hazen
05/16/2024, 9:04 PM--skip_md5sum
vs passing in a list of tools with --skip_tools
when skipping a process? My thoughts are that --skip_tools
should be used to skip a specific module and dedicated params should be about skipping subworkflows. Thoughts?Daniel G
05/17/2024, 6:27 AMSTAR(reads, index)
STAR_PASS2(reads, index, STAR.out.junctions.toSortedList())
I have tried various combinations of .toList()
, .collect()
etc. to see whether that fixes it, but none of them seem to work with -resume
. From what I can understand it might be that the junctions input might be in a different order between runs, but either even toSortedList()
hasn't worked. I have yet to try the fair: true
directive, but thought I might ask in here as well incase this was a known issue. I've seen some related issues here (https://github.com/nextflow-io/nextflow/issues/1475) where it had mentioned that collect()
should be resume safe, but from testing it out it doesn't seem to be in this case.