Comments (7)
Please could you provide the custom config used in the command, along with the sample and contrast sheets?
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Hi, sure. This is the sample sheet:
sample,condition,genome_bam
K562_TARDBP_TREATED_REP1,K562_TARDBP_TREATED,test-rnaseq/star_salmon/K562_TARDBP_TREATED_REP1.markdup.sorted.bam
K562_TARDBP_TREATED_REP2,K562_TARDBP_TREATED,test-rnaseq/star_salmon/K562_TARDBP_TREATED_REP2.markdup.sorted.bam
K562_TARDBP_CONTROL_REP1,K562_TARDBP_CONTROL,test-rnaseq/star_salmon/K562_TARDBP_CONTROL_REP1.markdup.sorted.bam
K562_TARDBP_CONTROL_REP2,K562_TARDBP_CONTROL,test-rnaseq/star_salmon/K562_TARDBP_CONTROL_REP2.markdup.sorted.bam
HepG2_TARDBP_TREATED_REP1,HepG2_TARDBP_TREATED,test-rnaseq/star_salmon/HepG2_TARDBP_TREATED_REP1.markdup.sorted.bam
HepG2_TARDBP_TREATED_REP2,HepG2_TARDBP_TREATED,test-rnaseq/star_salmon/HepG2_TARDBP_TREATED_REP2.markdup.sorted.bam
HepG2_TARDBP_CONTROL_REP1,HepG2_TARDBP_CONTROL,test-rnaseq/star_salmon/HepG2_TARDBP_CONTROL_REP1.markdup.sorted.bam
HepG2_TARDBP_CONTROL_REP2,HepG2_TARDBP_CONTROL,test-rnaseq/star_salmon/HepG2_TARDBP_CONTROL_REP2.markdup.sorted.bam
This is the contrast sheet:
contrast,treatment,control
K562_TARDBP_TREATED_CONTROL,K562_TARDBP_TREATED,K562_TARDBP_CONTROL
HepG2_TARDBP_TREATED_CONTROL,K562_TARDBP_TREATED,HepG2_TARDBP_CONTROL
And this is the custom.config. I only use it here to enforce running on HTCondor. Everything else in there so far is relevant to nf-core/sarek
.
// Function to ensure that resource requirements dont go beyond
// a maximum limit
process.executor = 'condor'
env.TILEDB_DISABLE_FILE_LOCKING='1'
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'time') {
try {
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'cpus') {
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {d
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}
}
}
process {
withName:'INDEX_CRAM|INDEX_MARKDUPLICATES|INDEX_MERGE_BAM|SAMTOOLS_INDEX|GATK4_APPLYBQSR|GATK4_BASERECALIBRATOR'{
cpus = { check_max( 1 * task.attempt, 'cpus' ) }
memory = { check_max( 3.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}
}
process {
withName:'BCFTOOLS_SORT|BCFTOOLS_STATS|SAMTOOLS_STATS|SAMTOOLS_MERGE|MERGE_BAM|INDEX_MERGE_BAM|GATK4_VARIANTRECALIBRATOR|GATK4_APPLYVQSR_INDEL|GATK4_APPLYVQSR_SNP|GATK4_APPLYVQSR|VARIANTRECALIBRATOR_INDEL|VARIANTRECALIBRATOR_SNP|TABIX_TABIX|TABIX|TABIX_BGZIPTABIX|TABIX_BGZIP_TIDDIT_SV'{
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 7.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}
}
process {
withName:'TABIX_BGZIPTABIX_INTERVAL_SPLIT|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS|GATK4_GENOTYPEGVCFS'{
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 7.GB * task.attempt, 'memory' ) }
time = { check_max( 24.h * task.attempt, 'time' ) }
}
}
process {
withName:'GATK4_MERGEVCFS|MERGE_GENOTYPEGVCFS|MERGE_VQSR|MERGE_MANTA_SMALL_INDELS|MERGE_MANTA_SV|MERGE_MANTA_DIPLOID|BWA_INDEX|BWAMEM2_INDEX'{
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 128.GB * task.attempt, 'memory' ) }
time = { check_max( 48.h * task.attempt, 'time' ) }
}
}
process {
withName:'FASTQC|MOSDEPTH|GATK4_HAPLOTYPECALLER|GATK4_GENOMICSDBIMPORT|CNVKIT_BATCH'{
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 15.GB * task.attempt, 'memory' ) }
time = { check_max( 12.h * task.attempt, 'time' ) }
}
}
process {
withName:'MANTA_GERMLINE|TIDDIT_SV'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 30.GB * task.attempt, 'memory' ) }
time = { check_max( 24.h * task.attempt, 'time' ) }
}
}
process {
withName:'FASTP|GATK4_MARKDUPLICATES|ENSEMBLVEP'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 30.GB * task.attempt, 'memory' ) }
time = { check_max( 48.h * task.attempt, 'time' ) }
}
}
process {
withName:'BWAMEM1_MEM|BWAMEM2_MEM|GATK4_MARKDUPLICATES_SPARK'{
cpus = { check_max( 16 * task.attempt, 'cpus' ) }
memory = { check_max( 60.GB * task.attempt, 'memory' ) }
time = { check_max( 24.h * task.attempt, 'time' ) }
}
}
process {
withName:'CNNSCOREVARIANTS'{
time = 336.h
}
}
trace {
enabled = true
fields = 'task_id,hash,native_id,name,status,exit,submit,start,complete,duration,realtime,%cpu,peak_rss,peak_vmem,rchar,wchar'
}
from rnasplice.
Thanks @amizeranschi, will get back to you after reviewing
from rnasplice.
Hi! Is there any update on this issue? It would be great to have this pipeline working from BAM files produced with nf-core/rnaseq, in order to avoid having to map reads a second time to the reference genome.
from rnasplice.
Hi @amizeranschi ,
We've just pushed a bunch of changes to dev, and this should have fixed your issue. Remember to force nextflow download the latest changes, rather than a cache of the one you currently have on your computer. Let us know how you get on.
from rnasplice.
Thanks @jma1991 for letting me know. I tried testing again and now I'm running into the issue described here: #72
Could you guys also implement the fixes proposed there by @dkoppstein and @valentinoruggieri?
from rnasplice.
Good that your issue has been solved. I will implement the fixes in #72 right now.
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Related Issues (20)
- link to example contrastsheet.csv is not working HOT 1
- Empty output for BAM+rMats HOT 2
- make contrasts file names consistent with those of the differentialabundance pipeline HOT 1
- Missing rMATS arguments HOT 2
- DEXSeq-DTU Stager pScreenAdjusted HOT 1
- sashimi_plot error HOT 2
- contrast file problem? HOT 7
- EXITING because of FATAL ERROR: Genome version: 20201 is INCOMPATIBLE with running STAR version: 2.7.9a HOT 2
- MISO error HOT 3
- The default --miso_genes are invalid when --gencode is specified and cause the pipeline to fail HOT 2
- EDGER_EXON fails if only single entry in contrast sheet HOT 1
- STAGER error: subscript out of bounds HOT 6
- The pipeline should be able to infer strandedness from FASTQ (i.e. allow "auto" for strandedness in the CSV) HOT 2
- Error with rmats.py when running with multiple contrasts: <filename>.bam not found in .rmats files HOT 10
- MISO_SASHIMI error: Could not find MISO output files HOT 4
- test profile: miso_index failure HOT 19
- example contrastsheet.csv missing HOT 1
- Add some more tags to make the pipeline easier to find HOT 1
- DRIMSEQ_FILTER error HOT 5
- STAGER error: subscript out of bounds HOT 4
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