From 6034cb2d8245c85d1c654176b4af1dbf76fed74b Mon Sep 17 00:00:00 2001 From: Mike Lloyd Date: Mon, 5 Aug 2024 10:44:12 -0400 Subject: [PATCH] v0.6.7 changes --- ReleaseNotes.md | 11 ++++++++++ bin/help/emase.nf | 2 ++ bin/help/gbrs.nf | 2 ++ bin/log/emase.nf | 3 +++ bin/log/gbrs.nf | 1 + modules/multiqc/multiqc.nf | 2 +- modules/python/python_merge_prep.nf | 2 +- modules/python/python_reorder_vcf_columns.nf | 2 +- modules/xengsort/xengsort_classify.nf | 22 +++++++++----------- nextflow.config | 2 +- run_scripts/README.md | 2 +- run_scripts/amplicon_human.sh | 2 +- run_scripts/atac_human.sh | 2 +- run_scripts/atac_mouse.sh | 2 +- run_scripts/chip_seq_human.sh | 2 +- run_scripts/chip_seq_mouse.sh | 2 +- run_scripts/emase.sh | 2 +- run_scripts/gbrs.sh | 2 +- run_scripts/generate_pseudoreference.sh | 2 +- run_scripts/germline_sv.sh | 2 +- run_scripts/prepare_emase.sh | 2 +- run_scripts/pta_human.sh | 2 +- run_scripts/pta_mouse.sh | 2 +- run_scripts/rnafusion_human.sh | 2 +- run_scripts/rnaseq_human.sh | 2 +- run_scripts/rnaseq_mouse.sh | 2 +- run_scripts/rnaseq_pdx.sh | 2 +- run_scripts/rrbs_human.sh | 2 +- run_scripts/rrbs_mouse.sh | 2 +- run_scripts/somatic_wes_pdx.sh | 2 +- run_scripts/wes_human.sh | 2 +- run_scripts/wes_mouse.sh | 2 +- run_scripts/wgs_human.sh | 2 +- run_scripts/wgs_mouse.sh | 2 +- subworkflows/pdx_rnaseq.nf | 1 + 35 files changed, 58 insertions(+), 40 deletions(-) diff --git a/ReleaseNotes.md b/ReleaseNotes.md index d4af0fd..eb4a536 100644 --- a/ReleaseNotes.md +++ b/ReleaseNotes.md @@ -1,5 +1,16 @@ # RELEASE NOTES +## Release 0.6.7 + +In this release we make the following minor adjustments: + +1. Correct syntax errors in the Xengsort module when running single-end data. +1. Minor adjustments to EMASE and GBRS help and log information to include the `gen_org` param. +1. Bump the version of MultiQC to v1.23. +1. Increase the memory request for a `PTA` moudles: `python_merge_prep.nf` and `python_reorder_vcf_columns.nf`. +1. Add `CHECK_STRANDEDNESS` to multiQC output for PDX RNAseq +1. Increased job memory request in example run scripts. + ## Release 0.6.6 In this release, we add a FASTQ sorting function to the Xengsort module. Due to asynchronous multi-threading in the classification step, Xengsort produces FASTQ output with non-deterministic sort order. BWA produces subtly different mapping results when reads in otherwise identical FASTQ inputs are shuffled ([see note from BWA developer here](https://github.com/lh3/bwa/issues/192#issuecomment-380612006)). The slight mapping differences are not enough to impact overall results, but do prevent fully reproducible results when Xengsort is used and reads are not sorted. The addition of the sorting function allows for fully reproducible results, with no additional user action required. diff --git a/bin/help/emase.nf b/bin/help/emase.nf index 457e1ca..ea89b50 100644 --- a/bin/help/emase.nf +++ b/bin/help/emase.nf @@ -24,6 +24,8 @@ Examples: Given the input file name "SAMPLE_NAME_1_OTHER_STUFF-WeDont_WANT.txt" if this `concat_sampleID_delim` = '_' and `concat_sampleID_positions` = "3" the sample ID would be assigned as `SAMPLE_NAME_1` Given the input file name "SAMPLE_NAME_1_OTHER_STUFF-WeDont_WANT.txt" if this `concat_sampleID_delim` = '-' and `concat_sampleID_positions` = "1" the sample ID would be assigned as `SAMPLE_NAME_1_OTHER_STUFF` +--genome_build | 'GRCm39' | Options: GRCm39 or GRCm38. + --bowtie_index | / | Path to the bowtie index. Include the bowtie prefix in this path (e.g., `/path/to/bowtie.transcripts` where bowtie.transcripts.* are the full set of index files in the directory. --transcripts_info | / | A file containing all transcript IDs. NOTE: These IDs must not contain haplotype IDs. This file must also have a 'length' column. Note that 'length' is not used in this context. ONLY IDs are used from this file. Can be obtained from `prepare_emase` workflow (emase.fullTranscripts.info) --gbrs_strain_list | | A list of haplotype names corresponding to genomes used in hybrid genome construction (e.g., 'A,B,C,D,E,F,G,H'). diff --git a/bin/help/gbrs.nf b/bin/help/gbrs.nf index f95d04d..5f243e7 100644 --- a/bin/help/gbrs.nf +++ b/bin/help/gbrs.nf @@ -24,6 +24,8 @@ Examples: Given the input file name "SAMPLE_NAME_1_OTHER_STUFF-WeDont_WANT.txt" if this `concat_sampleID_delim` = '_' and `concat_sampleID_positions` = "3" the sample ID would be assigned as `SAMPLE_NAME_1` Given the input file name "SAMPLE_NAME_1_OTHER_STUFF-WeDont_WANT.txt" if this `concat_sampleID_delim` = '-' and `concat_sampleID_positions` = "1" the sample ID would be assigned as `SAMPLE_NAME_1_OTHER_STUFF` +--genome_build | 'GRCm39' | Options: GRCm39 or GRCm38. + --bowtie_index | / | Path to the bowtie index. Include the bowtie prefix in this path (e.g., `/path/to/bowtie.transcripts` where bowtie.transcripts.* are the full set of index files in the directory. --transcripts_info | / | A file containing all transcript IDs. NOTE: These IDs must not contain haplotype IDs. This file must also have a 'length' column. Note that 'length' is not used in this context. ONLY IDs are used from this file. Can be obtained from `prepare_emase` workflow (emase.fullTranscripts.info) --gbrs_strain_list | | A list of haplotype names corresponding to genomes used in hybrid genome contrucution (e.g., 'A,B,C,D,E,F,G,H'). diff --git a/bin/log/emase.nf b/bin/log/emase.nf index b2cedb4..c872e2b 100644 --- a/bin/log/emase.nf +++ b/bin/log/emase.nf @@ -23,6 +23,7 @@ ______________________________________________________ --read_type ${params.read_type} --csv_input ${params.csv_input} --download_data ${params.download_data} +--genome_build ${params.genome_build} --bowtie_index ${params.bowtie_index} --transcripts_info ${params.transcripts_info} --gbrs_strain_list ${params.gbrs_strain_list} @@ -56,6 +57,7 @@ ______________________________________________________ --concat_lanes ${params.concat_lanes} --concat_sampleID_delim ${params.concat_sampleID_delim} --concat_sampleID_positions ${params.concat_sampleID_positions} +--genome_build ${params.genome_build} --bowtie_index ${params.bowtie_index} --transcripts_info ${params.transcripts_info} --gbrs_strain_list ${params.gbrs_strain_list} @@ -88,6 +90,7 @@ ______________________________________________________ --concat_lanes ${params.concat_lanes} --concat_sampleID_delim "N/A" --concat_sampleID_positions "N/A" +--genome_build ${params.genome_build} --bowtie_index ${params.bowtie_index} --transcripts_info ${params.transcripts_info} --gbrs_strain_list ${params.gbrs_strain_list} diff --git a/bin/log/gbrs.nf b/bin/log/gbrs.nf index e9c7f9a..3db8691 100644 --- a/bin/log/gbrs.nf +++ b/bin/log/gbrs.nf @@ -35,6 +35,7 @@ def param_log(){ --read_type ${params.read_type} --csv_input ${params.csv_input} --download_data ${params.download_data} + --genome_build ${params.genome_build} --bowtie_index ${params.bowtie_index} --transcripts_info ${params.transcripts_info} --gbrs_strain_list ${params.gbrs_strain_list} diff --git a/modules/multiqc/multiqc.nf b/modules/multiqc/multiqc.nf index e1560f4..870849a 100644 --- a/modules/multiqc/multiqc.nf +++ b/modules/multiqc/multiqc.nf @@ -5,7 +5,7 @@ process MULTIQC { errorStrategy {(task.exitStatus == 140) ? {log.info "\n\nError code: ${task.exitStatus} for task: ${task.name}. Likely caused by the task wall clock: ${task.time} or memory: ${task.memory} being exceeded.\nAttempting orderly shutdown.\nSee .command.log in: ${task.workDir} for more info.\n\n"; return 'finish'}.call() : 'finish'} - container 'quay.io/jaxcompsci/multiqc:v1.21_custom' + container 'quay.io/jaxcompsci/multiqc:v1.23_custom' publishDir "${params.pubdir}/multiqc", pattern: "*multiqc_report.html", mode:'copy' publishDir "${params.pubdir}/multiqc", pattern: "*_data", mode:'copy' diff --git a/modules/python/python_merge_prep.nf b/modules/python/python_merge_prep.nf index c2e5ebb..1458575 100644 --- a/modules/python/python_merge_prep.nf +++ b/modules/python/python_merge_prep.nf @@ -2,7 +2,7 @@ process MERGE_PREP { tag "$sampleID" cpus 1 - memory 4.GB + memory 10.GB time '04:00:00' errorStrategy {(task.exitStatus == 140) ? {log.info "\n\nError code: ${task.exitStatus} for task: ${task.name}. Likely caused by the task wall clock: ${task.time} or memory: ${task.memory} being exceeded.\nAttempting orderly shutdown.\nSee .command.log in: ${task.workDir} for more info.\n\n"; return 'finish'}.call() : 'finish'} diff --git a/modules/python/python_reorder_vcf_columns.nf b/modules/python/python_reorder_vcf_columns.nf index 1394c93..e039134 100644 --- a/modules/python/python_reorder_vcf_columns.nf +++ b/modules/python/python_reorder_vcf_columns.nf @@ -2,7 +2,7 @@ process REORDER_VCF_COLUMNS { tag "$sampleID" cpus 1 - memory 4.GB + memory 10.GB time '04:00:00' errorStrategy {(task.exitStatus == 140) ? {log.info "\n\nError code: ${task.exitStatus} for task: ${task.name}. Likely caused by the task wall clock: ${task.time} or memory: ${task.memory} being exceeded.\nAttempting orderly shutdown.\nSee .command.log in: ${task.workDir} for more info.\n\n"; return 'finish'}.call() : 'finish'} diff --git a/modules/xengsort/xengsort_classify.nf b/modules/xengsort/xengsort_classify.nf index 1c88f63..ad7db53 100644 --- a/modules/xengsort/xengsort_classify.nf +++ b/modules/xengsort/xengsort_classify.nf @@ -21,8 +21,8 @@ process XENGSORT_CLASSIFY { tuple val(sampleID), path(trimmed) output: - tuple val(sampleID), path("*fastq-graft_sorted.*.fq"), emit: xengsort_human_fastq - tuple val(sampleID), path("*fastq-host_sorted.*.fq"), emit: xengsort_mouse_fastq + tuple val(sampleID), path("*graft_sorted.*.fq"), emit: xengsort_human_fastq + tuple val(sampleID), path("*host_sorted.*.fq"), emit: xengsort_mouse_fastq tuple val(sampleID), path("*.txt"), emit: xengsort_log script: @@ -33,17 +33,16 @@ process XENGSORT_CLASSIFY { """ xengsort classify \ - --index ${xengsort_index}/${xengsort_index} \ + --index ${xengsort_index}/${params.xengsort_idx_name} \ --fastq ${trimmed[0]} \ --prefix ${sampleID} \ --mode count \ - --threads ${task.cpus} - --out fastq \ + --threads ${task.cpus} \ --chunksize 32.0 \ --compression none &> ${sampleID}_xengsort_log.txt - cat fastq-host.1.fq | paste - - - - | sort -k1,1 -t " " | tr "\\t" "\\n" > ${sampleID}_fastq-host_sorted.1.fq - cat fastq-graft.1.fq | paste - - - - | sort -k1,1 -t " " | tr "\\t" "\\n" > ${sampleID}_fastq-graft_sorted.1.fq + cat ${sampleID}-host.fq | paste - - - - | sort -k1,1 -t " " | tr "\\t" "\\n" > ${sampleID}-host_sorted.1.fq + cat ${sampleID}-graft.fq | paste - - - - | sort -k1,1 -t " " | tr "\\t" "\\n" > ${sampleID}-graft_sorted.1.fq """ @@ -58,15 +57,14 @@ process XENGSORT_CLASSIFY { --prefix ${sampleID} \ --mode count \ --threads ${task.cpus} \ - --out fastq \ --chunksize 32.0 \ --compression none &> ${sampleID}_xengsort_log.txt - cat fastq-host.1.fq | paste - - - - | sort -k1,1 -t " " | tr "\\t" "\\n" > ${sampleID}_fastq-host_sorted.1.fq - cat fastq-host.2.fq | paste - - - - | sort -k1,1 -t " " | tr "\\t" "\\n" > ${sampleID}_fastq-host_sorted.2.fq + cat ${sampleID}-host.1.fq | paste - - - - | sort -k1,1 -t " " | tr "\\t" "\\n" > ${sampleID}-host_sorted.1.fq + cat ${sampleID}-host.2.fq | paste - - - - | sort -k1,1 -t " " | tr "\\t" "\\n" > ${sampleID}-host_sorted.2.fq - cat fastq-graft.1.fq | paste - - - - | sort -k1,1 -t " " | tr "\\t" "\\n" > ${sampleID}_fastq-graft_sorted.1.fq - cat fastq-graft.2.fq | paste - - - - | sort -k1,1 -t " " | tr "\\t" "\\n" > ${sampleID}_fastq-graft_sorted.2.fq + cat ${sampleID}-graft.1.fq | paste - - - - | sort -k1,1 -t " " | tr "\\t" "\\n" > ${sampleID}-graft_sorted.1.fq + cat ${sampleID}-graft.2.fq | paste - - - - | sort -k1,1 -t " " | tr "\\t" "\\n" > ${sampleID}-graft_sorted.2.fq """ diff --git a/nextflow.config b/nextflow.config index bcbce08..1218ccc 100644 --- a/nextflow.config +++ b/nextflow.config @@ -45,7 +45,7 @@ manifest { homePage = "https://github.com/TheJacksonLaboratory/cs-nf-pipelines" mainScript = "main.nf" nextflowVersion = "!>=22.04.3" - version = "0.6.6" + version = "0.6.7" author = 'Michael Lloyd, Brian Sanderson, Barry Guglielmo, Sai Lek, Peter Fields, Harshpreet Chandok, Carolyn Paisie, Gabriel Rech, Ardian Ferraj, Anuj Srivastava. Copyright Jackson Laboratory 2024' } diff --git a/run_scripts/README.md b/run_scripts/README.md index 486a2c3..b73eaf9 100644 --- a/run_scripts/README.md +++ b/run_scripts/README.md @@ -13,7 +13,7 @@ Example: #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/amplicon_human.sh b/run_scripts/amplicon_human.sh index eba4c01..77706f0 100644 --- a/run_scripts/amplicon_human.sh +++ b/run_scripts/amplicon_human.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/atac_human.sh b/run_scripts/atac_human.sh index cd7d8a3..d9b86b7 100644 --- a/run_scripts/atac_human.sh +++ b/run_scripts/atac_human.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/atac_mouse.sh b/run_scripts/atac_mouse.sh index a831391..ab205d1 100644 --- a/run_scripts/atac_mouse.sh +++ b/run_scripts/atac_mouse.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/chip_seq_human.sh b/run_scripts/chip_seq_human.sh index bafbb34..f5bf103 100644 --- a/run_scripts/chip_seq_human.sh +++ b/run_scripts/chip_seq_human.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/chip_seq_mouse.sh b/run_scripts/chip_seq_mouse.sh index aee73f8..1c861a0 100644 --- a/run_scripts/chip_seq_mouse.sh +++ b/run_scripts/chip_seq_mouse.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/emase.sh b/run_scripts/emase.sh index 092cccd..0cd299a 100644 --- a/run_scripts/emase.sh +++ b/run_scripts/emase.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/gbrs.sh b/run_scripts/gbrs.sh index 7c367b9..4abf4db 100644 --- a/run_scripts/gbrs.sh +++ b/run_scripts/gbrs.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/generate_pseudoreference.sh b/run_scripts/generate_pseudoreference.sh index 1fff5bf..4d31e98 100644 --- a/run_scripts/generate_pseudoreference.sh +++ b/run_scripts/generate_pseudoreference.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/germline_sv.sh b/run_scripts/germline_sv.sh index c1118d9..c2b3a74 100644 --- a/run_scripts/germline_sv.sh +++ b/run_scripts/germline_sv.sh @@ -4,7 +4,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=2G +#SBATCH --mem=5G #SBATCH --ntasks=1 # LOAD NEXTFLOW diff --git a/run_scripts/prepare_emase.sh b/run_scripts/prepare_emase.sh index 037dec8..658d8e2 100644 --- a/run_scripts/prepare_emase.sh +++ b/run_scripts/prepare_emase.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/pta_human.sh b/run_scripts/pta_human.sh index d3ad311..e7afcac 100644 --- a/run_scripts/pta_human.sh +++ b/run_scripts/pta_human.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/pta_mouse.sh b/run_scripts/pta_mouse.sh index 9f7d241..7cfc338 100644 --- a/run_scripts/pta_mouse.sh +++ b/run_scripts/pta_mouse.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/rnafusion_human.sh b/run_scripts/rnafusion_human.sh index f394228..5d16df2 100644 --- a/run_scripts/rnafusion_human.sh +++ b/run_scripts/rnafusion_human.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/rnaseq_human.sh b/run_scripts/rnaseq_human.sh index e857ec2..8301b96 100644 --- a/run_scripts/rnaseq_human.sh +++ b/run_scripts/rnaseq_human.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/rnaseq_mouse.sh b/run_scripts/rnaseq_mouse.sh index fbae58d..c208ec6 100644 --- a/run_scripts/rnaseq_mouse.sh +++ b/run_scripts/rnaseq_mouse.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/rnaseq_pdx.sh b/run_scripts/rnaseq_pdx.sh index 82cb2f2..089ed17 100644 --- a/run_scripts/rnaseq_pdx.sh +++ b/run_scripts/rnaseq_pdx.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/rrbs_human.sh b/run_scripts/rrbs_human.sh index d34b220..170bca4 100644 --- a/run_scripts/rrbs_human.sh +++ b/run_scripts/rrbs_human.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/rrbs_mouse.sh b/run_scripts/rrbs_mouse.sh index 2aebac7..f9b6d23 100644 --- a/run_scripts/rrbs_mouse.sh +++ b/run_scripts/rrbs_mouse.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/somatic_wes_pdx.sh b/run_scripts/somatic_wes_pdx.sh index 8b3a965..3a618ca 100644 --- a/run_scripts/somatic_wes_pdx.sh +++ b/run_scripts/somatic_wes_pdx.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/wes_human.sh b/run_scripts/wes_human.sh index 6ec75f8..bf3be61 100644 --- a/run_scripts/wes_human.sh +++ b/run_scripts/wes_human.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/wes_mouse.sh b/run_scripts/wes_mouse.sh index 95944e9..345133d 100644 --- a/run_scripts/wes_mouse.sh +++ b/run_scripts/wes_mouse.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/wgs_human.sh b/run_scripts/wgs_human.sh index d5a5010..7c6a84d 100644 --- a/run_scripts/wgs_human.sh +++ b/run_scripts/wgs_human.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/run_scripts/wgs_mouse.sh b/run_scripts/wgs_mouse.sh index 9233e32..9526d47 100644 --- a/run_scripts/wgs_mouse.sh +++ b/run_scripts/wgs_mouse.sh @@ -5,7 +5,7 @@ #SBATCH -p compute #SBATCH -q batch #SBATCH -t 72:00:00 -#SBATCH --mem=1G +#SBATCH --mem=5G #SBATCH --ntasks=1 cd $SLURM_SUBMIT_DIR diff --git a/subworkflows/pdx_rnaseq.nf b/subworkflows/pdx_rnaseq.nf index a4de6bf..dfe9e89 100644 --- a/subworkflows/pdx_rnaseq.nf +++ b/subworkflows/pdx_rnaseq.nf @@ -128,6 +128,7 @@ workflow PDX_RNASEQ { ch_multiqc_files = ch_multiqc_files.mix(FASTP.out.quality_json.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.quality_stats.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(XENGSORT_CLASSIFY.out.xengsort_log.collect{it[1]}.ifEmpty([])) + ch_multiqc_files = ch_multiqc_files.mix(CHECK_STRANDEDNESS.out.strandedness_report.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(RSEM_ALIGNMENT_EXPRESSION_HUMAN.out.rsem_cnt.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(RSEM_ALIGNMENT_EXPRESSION_HUMAN.out.star_log.collect{it[1]}.ifEmpty([])) ch_multiqc_files = ch_multiqc_files.mix(PICARD_COLLECTRNASEQMETRICS_HUMAN.out.picard_metrics.collect{it[1]}.ifEmpty([]))