Hi guys.
I have a simple doubt (I think). I just need to save my output process in an external directory so I'm using the publishDir function for it. However I need 2 things: i) use variables (collected from input tuple); ii) Create the directory because it doesn't exist.
I successfully run it like this:
publishDir "${params.out_dir}/${tcga_project}/${tcga_barcode}/RSEM_quantification", mode: 'move'
input:
file STAR_bam_file from STAR_alignment_bam
set val(sample_UUID), val(tcga_barcode), val(tcga_project) from samples_ch_3But It doesn't create the directory. So I tried switching to this:
outDir = file("${params.out_dir}/${tcga_project}/${tcga_barcode}/RSEM_quantification")
outDir.mkdirs()
publishDir outDir, mode: 'move'
input:
file STAR_bam_file from STAR_alignment_bam
set val(sample_UUID), val(tcga_barcode), val(tcga_project) from samples_ch_3However it states the error of:No such variable: tcga_project
Any help in this situtation? Thanks :)
2 replies
-profile docker at the command line level, and instead I would like to have in my nextflow.config file profile = docker such that it successfully imports all of the config options specified by the docker profile. thanks
3 replies
collectFile in my workflow to combine the results of several upstream processes, and setting storeDir. However, when I resume my workflow (using AWS Batch executor), even though the upstream processes are correctly cached, the downstream process that consumes the output of collectFile always re-executes. I've tried sorting the input to collectFile with no luck.
4 replies
3 replies
How come
Channel
.fromFilePairs( "${params.reads}/*{1,2}*.fastq.gz", size: 2 )
.into { paired_reads }does not work when the file starts with a number (like 7126-MS-1_100_S1_L005_R1_001.fastq.gz and 7126-MS-1_100_S1_L005_R2_001.fastq.gz or 21VR067049-211104_S1_L001_R1_001.fastq.gz and21VR067049-211104_S1_L001_R2_001.fastq.gz
8 replies
.collate() in my pipeline and then an implementation of this which works elegantly. My problem is with the -resume option. Some processes get cached, but the rest are re-scheduled. I am assuming the order changes from run to run before the collate operator, and thus assumes input has changed. Could this be it?
Channel.from(2,1,3,4).toSortedList().fromList()
Hello Group members, I am trying a sample nextflow script using Azure Blob storage for work directory. I am getting an error and couldn't understand if my setup has anything to do, appreciate your response. Here is the error when trying to run my sample script connecting to Azure Blob storage
nextflow run tutorial.nf -w az://nextflow-work/work
3 replies
How to deal with the empty path channel in process (dsl2)? I saw a solution for empty channel of value (https://github.com/nextflow-io/patterns/blob/master/docs/process-when-empty.adoc)
nextflow.enable.dsl=2
params.a = '*.txt'
params.b = ''
params.c = ''
process test {
tag "test "
echo true
input:
path file1
path file2
val value1
"""
echo $file1
echo $file2
echo $value1
"""
}
workflow {
a_ch = Channel.fromPath(params.a)
b_ch = Channel.fromPath(params.b)
test(a_ch,b_ch,params.c)
}The Error message:
N E X T F L O W ~ version 21.04.3
Launching `code/test2.nf` [modest_colden] - revision: b4078eef6a
Missing `fromPath` parameter
a_ch = params.a ? Channel.fromPath(params.a) : [] maybe?
1 reply
Hi,
I'm trying to use Docker in Nextflow script and I'm getting the following error:
"connect to the Docker daemon socket at unix:///var/run/docker.sock: Post "http://%2Fvar%2Fr
un%2Fdocker.sock/v1.24/containers/create?name=nxf-8IoBF1Fj7HBmfAtOGRGpW5Fp": dial unix /var/run/docker.sock: connect: permission denied.
See 'docker run --help'."
Does anyone have any advice on how to handle this?
:point_up: Edit: Hi,
I'm trying to use Docker in Nextflow script and I'm getting the following error:
"connect to the Docker daemon socket at unix:///var/run/docker.sock: Post "http://%2Fvar%2Fr
un%2Fdocker.sock/v1.24/containers/create?name=nxf-8IoBF1Fj7HBmfAtOGRGpW5Fp": dial unix /var/run/docker.sock: connect: permission denied.
See 'docker run --help'."Does anyone have any advice on how to handle this?
2 replies
Hello,
I am trying to run nextflow inside a docker and from there: run other dockers in the host machine. For that I have built a docker image with nextflow and docker inside, as so:
FROM nextflow/nextflow
# Adds ability to run docker in the host
RUN amazon-linux-extras install docker -y
WORKDIR /nextflowBut when running the below line, it says Command error: /bin/bash: .command.sh: No such file or directory
docker run -v /var/run/docker.sock:/var/run/docker.sock custom/nextflow bash -c 'nextflow run hello -with-docker nextflow/examples'Does anyone have an idea on how to fix this?
publish command? I understand it is asynchronous by default, but I have a pipeline that runs for 7-10 days and some of the useful results are complete after the first day. Would be good if I could request the results from day 1 are "published" soon after completion.
Process
init_Config (3) terminated for an unknown reason -- Likely it has been terminated by theexternal system
Looking at the log files of the other 'init_Config' processes, nothing differentiates them. No error flags around wall-time or ressource usage. How do you trouble-shoot that?
Hello everyone,
Is it possible to update process information using withLabel on the command line? So something like:
nextflow run hello_world.nf -process.withLabel:hello_world.cpus 2
I know that something as simple as this works:
nextflow run hello_world.nf -process.cpus 2
but I want to target a particular process.
hello everyone, I am using singularity images from biocontainers for most of my processes, where they are pre-downloaded and used directly (as the cluster nodes don't have internet access). However, I am having issues with the Prokka image from that site. I pull the images from biocontainers with singularity pull, and use that image directly in the nextflow pipeline. However, it seems that nextflow doesn't want to use the prokka image directly, it rather wants to download it from docker. Note that it works fine for all other processes that have been downloaded the same way. Does anyone know anything about this image? https://biocontainers.pro/tools/prokka
(Note: I have tried several versions of the singularity image, all give the same result).
My nextflow.config:
params.container_dir = 'path/to/images'
singularity {
enabled = true
autoMounts = true
}The container is called like this in the prokka process:
process PROKKA {
container "${container_dir}/prokka:1.14.5--pl526_1"Thanks in advance!
Hello,
I am trying to figure out how to separate and categorize some files based on some string values in their name. For example, if the files are named;
X_filename_f0_r1-1_1_R1.fastq
X_filename_f0_r0-1_1_R1.fastq
X_filename_f0_r0-1_2_R1.fastq
X_filename_f0_r1-0_3_R1.fastq
X_filename_f1_r1-1_1_R1.fastq
X_filename_f1_r0-1_1_R1.fastq
X_filename_f1_r0-1_2_R1.fastq
X_filename_f1_r1-0_3_R1.fastq
X_filename_f2_r1-1_1_R1.fastq
X_filename_f2_r0-1_1_R1.fastq
X_filename_f2_r0-1_2_R1.fastq
X_filename_f2_r1-0_3_R1.fastq
X_filename_f3_r1-1_1_R1.fastq
X_filename_f3_r0-1_1_R1.fastq
X_filename_f3_r0-1_2_R1.fastq
X_filename_f3_r1-0_3_R1.fastq
How can I separate the files based on f0, f1, f2, f3 and have each category saved under a different name? Then I want to separate the same files based on the numbers after the "r" but before the underscore. There are a lot of different numbers so I can't be specific in the script about the numbers to select. These same files will then be separated again based on the number before "_R1". So in the end, I will have a category of files based on f-number then a subcategory based on r number then another subcategory under that based on a number.
Thanks
Tj
Hi all,
My challenge of my code is to create input for pairwise comparison. Based on the comparison list, I would like to select the samples that are in that group. I have tried the following but not with complete success as I receive a DataflowBroadcast around DataflowStream[?]
bams = Channel.from(["sampleX_1", "groupX", "bamX_1", "baiX_1"],
["sampleX_2", "groupX", "bamX_2", "baiX_2"],
["sampleY_1", "groupY", "bamY_1", "baiY_1"],
["sampleY_2", "groupY", "bamY_2", "baiY_2"],
["sampleZ_1", "groupZ", "bamZ_1", "baiZ_1"],
["sampleZ_2", "groupZ", "bamZ_2", "baiZ_2"])
comparison_list = Channel.from(["groupX", "groupY"],["groupX", "groupZ"])
group_input = comparison_list_file.map{ it ->
def bam_by_group = bam.groupTuple(by:1)
def compare1 = it[0]
def compare2 = it[1]
def group_ctrl = bam_by_group.first{ it[1] == compare1}
def group_case = bam_by_group.first{ it[1] == compare2}
def group_input = group_ctrl.combine(group_case)
return group_input.view() // - desired outcome, see below
}.view() // results into - DataflowBroadcast around DataflowStream[?]I like the result to have it in this format:
// [[sampleX_1, sampleX_2], groupX, [bamX_1, bamX_2], [baiX_1, baiX_2], [sampleY_1, sampleY_2], groupY, [bamY_1, bamY_2], [baiY_1, baiY_2]]
// [[sampleX_1, sampleX_2], groupX, [bamX_1, bamX_2], [baiX_1, baiX_2], [sampleZ_1, sampleZ_2], groupZ, [bamZ_1, bamZ_2], [baiZ_1, baiZ_2]]Of which group_input.view() does but how can I use that?
Thanks!
On a related note, I'm trying to group process outputs together for downstream paired processing. I have a digest file that looks like
sample_id,read1,read2,control_id
cell1_ctl,A.fq.gz,B.fq.gz,
cell1_trt1,C.fq.gz,D.fq.gz,cell1_ctl
cell1_trt2,E.fq.gz,F.fq.gz,cell1_ctl
cell2_ctl,G.fq.gz,H.fg.gz,
cell2_trt1,I.fq.gz,J.fq.gz,cell2_ctl
cell2_trt2,K.fq.gz,L.fq.gz,cell2_ctland I have a basic pipeline that drives from per-column channels and looks like
aln_bams = bwamem(samples_ch, read1_ch, read2_ch)
filt_bams = mapq_filter(aln_bams, 30)but now i need to get to bam channels that look like
[cell1_trt1.bam, cell1_trt2.bam, cell2_trt1.bam, cell2_trt2.bam]
[cell1_ctl.bam, cell1_ctl.bam, cell2_ctl.bam, cell2_ctl.bam]the issue is I can't find a way to join the filtered bams with the original IDs. In DSL=1, I could merge; but using DSL=2 I need an index on which to join, and there's no such thing as .mapWithIndex.
Any ideas?
2 replies
is there any usage example for this. nextflow-io/nextflow#524
I did
process {
cpus = 4
withLabel:test2 {
publish_dir = 'result_data'
}
}And got the following warning
WARN: Access to undefined parameter `publish_dir` -- Initialise it to a default value eg. `params.publish_dir = some_value`
WARN: Process `test2` publishDir path contains a variable with a null value
WARN: Process `test2` publishDir path contains a variable with a null value
WARN: Process `test2` publishDir path contains a variable with a null value
WARN: Process `test2` publishDir path contains a variable with a null value
WARN: Process `test2` publishDir path contains a variable with a null value
6 replies
Hi all,
My challenge of my code is to create input for pairwise comparison. Based on the comparison list, I would like to select the samples that are in that group. I have tried the following but not with complete success as I receive a
DataflowBroadcast around DataflowStream[?]bams = Channel.from(["sampleX_1", "groupX", "bamX_1", "baiX_1"], ["sampleX_2", "groupX", "bamX_2", "baiX_2"], ["sampleY_1", "groupY", "bamY_1", "baiY_1"], ["sampleY_2", "groupY", "bamY_2", "baiY_2"], ["sampleZ_1", "groupZ", "bamZ_1", "baiZ_1"], ["sampleZ_2", "groupZ", "bamZ_2", "baiZ_2"]) comparison_list = Channel.from(["groupX", "groupY"],["groupX", "groupZ"]) group_input = comparison_list_file.map{ it -> def bam_by_group = bam.groupTuple(by:1) def compare1 = it[0] def compare2 = it[1] def group_ctrl = bam_by_group.first{ it[1] == compare1} def group_case = bam_by_group.first{ it[1] == compare2} def group_input = group_ctrl.combine(group_case) return group_input.view() // - desired outcome, see below }.view() // results into - DataflowBroadcast around DataflowStream[?]I like the result to have it in this format:
// [[sampleX_1, sampleX_2], groupX, [bamX_1, bamX_2], [baiX_1, baiX_2], [sampleY_1, sampleY_2], groupY, [bamY_1, bamY_2], [baiY_1, baiY_2]] // [[sampleX_1, sampleX_2], groupX, [bamX_1, bamX_2], [baiX_1, baiX_2], [sampleZ_1, sampleZ_2], groupZ, [bamZ_1, bamZ_2], [baiZ_1, baiZ_2]]Of which
group_input.view()does but how can I use that?Thanks!
I modified map_join function created by multimeric (nextflow-io/nextflow#559). I extended to function to "loop over" the keys and it worked!
Is there a way to specify a custom path for the
.nextflow.log file in the nextflow.config file? I know it's possible on the command-line using the -log option but I would like to specify it in the nextflow.config so I can modify the path based on our params.outdir parameter.
How to specify the thread value in nextflow script for sge jobs?
For local jobs, cpu information is provided using the following configuration settings.
process {
cpus = 12
}And after that that value is used in $task.cpus variable. But in can of SGE executor, the cpus variable is not allowed. So I provided threads using -pe option. But unable to access that value in the script.
Here is my configuration setup.
process {
executor = 'sge'
clusterOptions = '-V -pe threaded 13'
}So, can someone suggest a solution for this. Thanks in advance.
hi, all. I am brand-new to nextflow. Just recently installed nextflow on my local computer and ran into the follow error. Here is my code,
num = Channel.from( 1, 2, 3 )
process test {
input:
val num
script:
println "echo process test $num"
}
`Here is my error: N E X T F L O W ~ version 21.10.0
Launching process.nf [irreverent_feynman] - revision: 386318b60a
executor > local (3)
executor > local (3)
[b7/c314a2] process > test (1) [100%] 3 of 3, failed: 3 ✘
echo process test 2
echo process test 1
echo process test 3
Error executing process > 'test (3)'
Caused by:
Process test (3) terminated with an error exit status (127)
Command executed:
null
Command exit status:
127
Command output:
(empty)
Command error:
.command.sh: line 2: null: command not found
Work dir:
/Users/limin/limin_practice/nextflow/work/37/b1c3dd131fb6078750b0f16150fe40
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
Can anyone help me understand what does the error message mean? How should I correct my codes?
5 replies
We're currently using the basic strategy described in the docs like
memory { 2.GB * task.attempt }, with separate labels that use the same retry-with-increased-resources strategy (like low_mem and high_mem) to coarsely indicate the size of the job. The label definitions are specified in the configuration file, and the labels are applied in the process file.Is there a way to keep the "strategy" in the config file (
x.GB * task.attempt), while the actual amount (2.GB, etc) varies based on some calculation done by the process directive?Or is the strategy something I should be writing a function for, and then applying to the closure that calculates the value? Like
memory (retryFunc { inputfile.size * 3 })
after upgrading Nextflow 21.04.3 to 21.10.3 my workflow fails with the following error:
groovy.lang.MissingMethodException: No signature of method: nextflow.script.WorkflowDef.nr_records() is applicable for argument types: ([Ljava.lang.Object;) values: [[/gro
ups/solve-rd/tmp10/projects/vip/nextflow/git/vip/test/output/test_snv/.nxf_work/92/1158ff50d7175029ff592f11a241f3/snv_prepared.vcf.gz.stats]]
at nextflow.script.WorkflowParamsResolver.invokeMethod(WorkflowDef.groovy:217)def nr_records(statsFilePath) {
...
} channel.fromPath(params.input) \
| prepare \
| branch {
small: nr_records(it.last()) <= params.chunk_size
large: true
}
...process prepare {
...
output:
tuple ..., path("${vcfOutputPath}.stats")
...I've tried updating in the caller and callee in various ways without success. does anyone have a clue what changed between Nextflow versions?
2 replies
Hello, I installed next flow in the computing cluster but I am not able to use the docker files required for running deep variant analysis. I used the following command: nextflow run nf-core/deepvariant -profile test,docker
N E X T F L O W ~ version 21.10.4
Launching nf-core/deepvariant [lethal_tesla] - revision: 2b5486356c [master]
Downloading plugin nf-amazon@1.3.4
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'nf-core/deepvariant v1.0"
Pipeline Name : nf-core/deepvariant
Pipeline Version: 1.0
Bam file : https://github.com/nf-core/test-datasets/raw/deepvariant/testdata/NA12878_S1.chr20.10_10p1mb.bam
Bed file : https://github.com/nf-core/test-datasets/raw/deepvariant/testdata/test_nist.b37_chr20_100kbp_at_10mb.bed
Reference genome: hg19chr20
Fasta Ref : s3://deepvariant-data/genomes/hg19chr20/chr20.fa
Fasta Index : s3://deepvariant-data/genomes/hg19chr20/chr20.fa.fai
Fasta gzipped : s3://deepvariant-data/genomes/hg19chr20/chr20.fa.gz
Fasta gzipped Index: s3://deepvariant-data/genomes/hg19chr20/chr20.fa.gz.fai
Fasta bgzip Index: s3://deepvariant-data/genomes/hg19chr20/chr20.fa.gz.gzi
Max Memory : 6 GB
Max CPUs : 2
Max Time : 2d
Model : wgs
Output dir : results
Working dir : /scicore/home/cichon/thirun0000/my-pipelines/nf-core/deepvariant-master/work
Container Engine: docker
Container : nfcore/deepvariant:1.0
Current home : /scicore/home/cichon/thirun0000
Current user : thirun0000
Current path : /scicore/home/cichon/thirun0000/my-pipelines/nf-core/deepvariant-master
Script dir : /scicore/home/cichon/thirun0000/.nextflow/assets/nf-core/deepvariant
Config Profile : test,docker
executor > local (1)
[- ] process > preprocess_bam -
[- ] process > make_examples -
[- ] process > call_variants -
[- ] process > postprocess_variants -
[e7/dec5cb] process > get_software_versions [100%] 1 of 1, failed: 1 ✘
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'get_software_versions'
Caused by:
Process get_software_versions terminated with an error exit status (127)
Command executed:
echo 1.0 &> v_nf_deepvariant.txt
echo 21.10.4 &> v_nextflow.txt
ls /opt/conda/pkgs/ &> v_deepvariant.txt
python --version &> v_python.txt
pip --version &> v_pip.txt
samtools --version &> v_samtools.txt
lbzip2 --version &> v_lbzip2.txt
bzip2 --version &> v_bzip2.txt
scrape_software_versions.py &> software_versions_mqc.yaml
Command exit status:
127
Command output:
(empty)
Command error:
.command.run: line 279: docker: command not found
Work dir:
/scicore/home/cichon/thirun0000/my-pipelines/nf-core/deepvariant-master/work/e7/dec5cbd65b63e4fdd5ccced4f1e516
Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run
Fastagz file not found: s3://deepvariant-data/genomes/hg19chr20/chr20.fa.gz
Fai file not found: s3://deepvariant-data/genomes/hg19chr20/chr20.fa.fai
gzfai file not found: s3://deepvariant-data/genomes/hg19chr20/chr20.fa.gz.fai
please specify --bed option (--bed bedfile)
https://github.com/nf-core/test-datasets/raw/deepvariant/testdata/NA12878_S1.chr20.10_10p1mb.bam not found
gzi file not found: s3://deepvariant-data/genomes/hg19chr20/chr20.fa.gz.gzi
hello
is it possible to make iteration over processes in dsl2 ?, as in https://github.com/nextflow-io/patterns/blob/master/docs/feedback-loop.adoc
what I tried doesn't work
(to annotate vcf with several databases)
take:
entrees_vcf // tuple [info1, info2, info3, vcf]
bdds // collection of collections: [ [bdd1,index1,tag1,fields1], [bdd2,index2,tag2,fields2], ...]
main:
input_ch = input_vcf
.concat( bdds.map{it[0]}, Channel.of(0) ).flatten().toList()
.mix(
Annotation_bdd_vcf.out
.concat( bdds )
.toList()
.map { ch_tuple, bdds ->
if ( ch_tuple[4] < bdds.size() ) { //(bdds[iteration]) {
return [ ch_tuple[0], ch_tuple[1], ch_tuple[2], ch_tuple[3], bdds[iteration], ch_tuple[4] ].flatten()
}
}
)
Annotation_bdd_vcf( input_ch )in Annotation_bdd_vcf input, the last variable (coming from Channel.of(0)) is incremented each time the process is executed
4 replies
-M option) and the only thing that is mentioned in the documentation and the issues is using env.SLURM_CLUSTERS. Unfortunately as I am reading in another issue (and I have confirmed by trying) that is not valid in a process { withLabel: xxx {cant put env here}} selector block. Is my only option a PR?