Background
The CARLISLE pipeline was developed in support of NIH Dr Vassiliki Saloura's Laboratory and Dr Javed Khan's Laboratory. It has been developed and tested solely on NIH HPC Biowulf.
Last update: 2024-02-21
The CARLISLE pipeline was developed in support of NIH Dr Vassiliki Saloura's Laboratory and Dr Javed Khan's Laboratory. It has been developed and tested solely on NIH HPC Biowulf.
"},{"location":"user-guide/contributions/","title":"Contributions","text":"The following members contributed to the development of the CARLISLE pipeline:
- Samantha Sevilla
- Vishal Koparde
- Hsien-chao Chou
- Sohyoung Kim
- Yue Hu
- Vassiliki Saloura
VK, SS, SK, HC contributed to the generating the source code and all members contributed to the main concepts and analysis.
"},{"location":"user-guide/getting-started/","title":"Overview","text":"The CARLISLE github repository is stored locally, and will be used for project deployment. Multiple projects can be deployed from this one point simultaneously, without concern.
"},{"location":"user-guide/getting-started/#1-getting-started","title":"1. Getting Started","text":""},{"location":"user-guide/getting-started/#11-introduction","title":"1.1 Introduction","text":"The CARLISLE Pipelie beings with raw FASTQ files and performs trimming followed by alignment using BOWTIE2. Data is then normalized through either the use of an user-species species (IE E.Coli) spike-in control or through the determined library size. Peaks are then called using MACS2, SEACR, and GoPEAKS with various options selected by the user. Peaks are then annotated, and summarized into reports. If designated, differential analysis is performed using DESEQ2. QC reports are also generated with each project using FASTQC and MULTIQC. Annotations are added using HOMER and ROSE. GSEA Enrichment analysis predictions are added using CHIPENRICH.
The following are sub-commands used within CARLISLE:
- initialize: initalize the pipeline
- dryrun: predict the binding of peptides to any MHC molecule
- cluster: execute the pipeline on the Biowulf HPC
- local: execute a local, interactive, session
- git: execute GitHub actions
- unlock: unlock directory
- DAG: create DAG report
- report: create SNAKEMAKE report
- runtest: copies test manifests and files to WORKDIR
CARLISLE has several dependencies listed below. These dependencies can be installed by a sysadmin. All dependencies will be automatically loaded if running from Biowulf.
- bedtools: \"bedtools/2.30.0\"
- bedops: \"bedops/2.4.40\"
- bowtie2: \"bowtie/2-2.4.2\"
- cutadapt: \"cutadapt/1.18\"
- fastqc: \"fastqc/0.11.9\"
- fastq_screen: \"fastq_screen/0.15.2\"
- fastq_val: \"/data/CCBR_Pipeliner/iCLIP/bin/fastQValidator\"
- fastxtoolkit: \"fastxtoolkit/0.0.14\"
- gopeaks: \"github clone https://github.com/maxsonBraunLab/gopeaks\"
- macs2: \"macs/2.2.7.1\"
- multiqc: \"multiqc/1.9\"
- perl: \"perl/5.34.0\"
- picard: \"picard/2.26.9\"
- python37: \"python/3.7\"
- R: \"R/4.2.2\"
- rose: \"ROSE/1.3.1\"
- samtools: \"samtools/1.15\"
- seacr: \"seacr/1.4-beta.2\"
- ucsc: \"ucsc/407\"
CARLISLE has been exclusively tested on Biowulf HPC. Login to the cluster's head node and move into the pipeline location.
# ssh into cluster's head node\nssh -Y $USER@biowulf.nih.gov\nAn interactive session should be started before performing any of the pipeline sub-commands, even if the pipeline is to be executed on the cluster.
# Grab an interactive node\nsinteractive --time=12:00:00 --mem=8gb --cpus-per-task=4 --pty bash\nThe following directories are created under the WORKDIR/results directory:
- alignment_stats: this directory include information on the alignment of each sample
- bam: this directory includes BAM files, statistics on samples, statistics on spike-in controls for each sample
- bedgraph: this directory includes BEDGRAPH files and statistic summaries for each sample
- bigwig: this directory includes the bigwig files for each sample
- peaks: this directory contains a sub-directory that relates to the quality threshold used.
- quality threshold
- contrasts: this directory includes the contrasts for each line listed in the contrast manifest
- peak_caller: this directory includes all peak calls from each peak_caller (SEACR, MACS2, GOPEAKS) for each sample
- annotation
- go_enrichment: this directory includes gene set enrichment pathway predictions
- homer: this directory includes the annotation output from HOMER
- rose: this directory includes the annotation output from ROSE
- annotation
- quality threshold
- qc: this directory includes MULTIQC reports and spike-in control reports (when applicable)
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\u2502\u00a0\u00a0 \u2514\u2500\u2500 contrast_id2.dedup_status.go_enrichment_html_report\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 homer\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id1_vs_control_id.dedup_status.gopeaks_broad.motifs\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 homerResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 knownResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id1_vs_control_id.dedup_status.gopeaks_narrow.motifs\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 homerResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 knownResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id2_vs_control_id.dedup_status.gopeaks_broad.motifs\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 homerResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 knownResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id2_vs_control_id.dedup_status.gopeaks_narrow.motifs\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 homerResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 knownResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 rose\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id1_vs_control_id.dedup_status.gopeaks_broad.12500\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id1_vs_control_id.dedup_status.gopeaks_narrow.12500\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id2_vs_control_id.dedup_status.dedup.gopeaks_broad.12500\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id2_vs_control_id.dedup_status.dedup.gopeaks_narrow.12500\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 peak_output\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 macs2\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 annotation\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 go_enrichment\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 contrast_id1.dedup_status.go_enrichment_tables\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 contrast_id2.dedup_status.go_enrichment_html_report\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 homer\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id1_vs_control_id.dedup_status.macs2_narrow.motifs\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 homerResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 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\u2502\u00a0\u00a0 \u2514\u2500\u2500 knownResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id2_vs_control_id.dedup_status.macs2_broad.motifs\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 homerResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 knownResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 rose\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id1_vs_control_id.dedup_status.macs2_broad.12500\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id1_vs_control_id.dedup_status.macs2_narrow.12500\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id2_vs_control_id.dedup_status.macs2_broad.12500\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id2_vs_control_id.dedup_status.macs2_narrow.12500\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 peak_output\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 seacr\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 annotation\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 go_enrichment\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 contrast_id1.dedup_status.go_enrichment_tables\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 contrast_id2.dedup_status.go_enrichment_html_report\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 homer\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id1_vs_control_id.dedup_status.seacr_non_relaxed.motifs\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 homerResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 knownResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id1_vs_control_id.dedup_status.seacr_non_stringent.motifs\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 homerResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 knownResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id1_vs_control_id.dedup_status.seacr_norm_relaxed.motifs\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 homerResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 knownResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id1_vs_control_id.dedup_status.seacr_norm_stringent.motifs\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 homerResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 knownResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id2_vs_control_id.dedup_status.seacr_non_relaxed.motifs\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 homerResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 knownResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id2_vs_control_id.dedup_status.seacr_non_stringent.motifs\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 homerResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 knownResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id2_vs_control_id.dedup_status.seacr_norm_relaxed.motifs\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 homerResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 knownResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id2_vs_control_id.dedup_status.seacr_norm_stringent.motifs\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 homerResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 knownResults\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 rose\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id1_vs_control_id.dedup_status.seacr_non_relaxed.12500\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id1_vs_control_id.dedup_status.seacr_non_stringent.12500\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id1_vs_control_id.dedup_status.seacr_norm_relaxed.12500\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id1_vs_control_id.dedup_status.seacr_norm_stringent.12500\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id2_vs_control_id.dedup_status.seacr_non_relaxed.12500\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id2_vs_control_id.dedup_status.seacr_non_stringent.12500\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id2_vs_control_id.dedup_status.seacr_norm_relaxed.12500\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u251c\u2500\u2500 replicate_id2_vs_control_id.dedup_status.seacr_norm_stringent.12500\n\u2502\u00a0\u00a0 \u2502\u00a0\u00a0 \u2514\u2500\u2500 peak_output\n\u2514\u2500\u2500 qc\n \u251c\u2500\u2500 fastqc_raw\n \u2514\u2500\u2500 fqscreen_raw\nThe pipeline is controlled through editing configuration and manifest files. Defaults are found in the /WORKDIR/config and /WORKDIR/manifest directories, after initialization.
"},{"location":"user-guide/preparing-files/#21-configs","title":"2.1 Configs","text":"The configuration files control parameters and software of the pipeline. These files are listed below:
- config/config.yaml
- resources/cluster.yaml
- resources/tools.yaml
The cluster configuration file dictates the resouces to be used during submission to Biowulf HPC. There are two differnt ways to control these parameters - first, to control the default settings, and second, to create or edit individual rules. These parameters should be edited with caution, after significant testing.
"},{"location":"user-guide/preparing-files/#212-tools-config","title":"2.1.2 Tools Config","text":"The tools configuration file dictates the version of each software or program that is being used in the pipeline.
"},{"location":"user-guide/preparing-files/#213-config-yaml","title":"2.1.3 Config YAML","text":"There are several groups of parameters that are editable for the user to control the various aspects of the pipeline. These are :
- Folders and Paths
- These parameters will include the input and ouput files of the pipeline, as well as list all manifest names.
- User parameters
- These parameters will control the pipeline features. These include thresholds and whether to perform processes.
- References
- These parameters will control the location of index files, spike-in references, adaptors and species calling information.
The pipeline allows for the use of a species specific spike-in control, or the use of normalization via library size. The parameter spikein_genome should be set to the species term used in spikein_reference.
For example for ecoli spike-in:
run_contrasts: \"Y\"\nnorm_method: \"spikein\"\nspikein_genome: \"ecoli\"\nspikein_reference:\n ecoli:\n fa: \"PIPELINE_HOME/resources/spikein/Ecoli_GCF_000005845.2_ASM584v2_genomic.fna\"\nFor example for drosophila spike-in:
run_contrasts: \"Y\"\nnorm_method: \"spikein\"\nspikein_genome: \"drosophila\"\nspikein_reference:\n drosophila:\n fa: \"/fdb/igenomes/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa\"\nIf it's determined that the amount of spike-in is not sufficient for the run, a library normaliaztion can be performed. 1. Complete a CARLISLE run with spike-in set to \"Y\". This will allow for the complete assessment of the spike-in. 2. Run inital QC analysis on the output data 3. Add the alignment_stats dir to the configuration file. 4. Re-run the CARLISLE pipeline
"},{"location":"user-guide/preparing-files/#21312-duplication-status","title":"2.1.3.1.2 Duplication Status","text":"Users can select duplicated peaks (dedup) or non-deduplicated peaks (no_dedup) through the user parameter.
dupstatus: \"dedup, no_dedup\" \nThree peak callers are available for deployment within the pipeline, with different settings deployed for each caller.
- MACS2 is available with two peak calling options: narrowPeak or broadPeak. NOTE: DESeq step generally fails for broadPeak; generally has too many calls.
peaktype: \"macs2_narrow, macs2_broad,\"\n - SEACR is available with four peak calling options: stringent or relaxed parameters, to be paired with \"norm\" for samples without a spike-in control and \"non\" for samples with a spikein control
peaktype: \"seacr_stringent, seacr_relaxed\"\n - GOPEAKS is available with two peak calling options: narrowpeaks or broadpeaks
A complete list of the available peak calling parameters and the recommended list of parameters is provided below:peaktype: \"gopeaks_narrow, gopeaks_broad\"\n
# Recommended list\n### peaktype: \"macs2_narrow, macs2_broad, gopeaks_narrow, gopeaks_broad\"\n\n# Available list\n### peaktype: \"macs2_narrow, macs2_broad, seacr_norm_stringent, seacr_norm_relaxed, seacr_non_stringent, seacr_non_relaxed, gopeaks_narrow, gopeaks_broad\"\nMACS2 can be run with or without the control. adding a control will increase peak specificity Selecting \"Y\" for the macs2_control will run the paired control sample provided in the sample manifest
Thresholds for quality can be controled through the quality_tresholds parameter. This must be a list of comma separated values. minimum of numeric value required.
- default MACS2 qvalue is 0.05 https://manpages.ubuntu.com/manpages/xenial/man1/macs2_callpeak.1.html
- default GOPEAKS pvalue is 0.05 https://github.com/maxsonBraunLab/gopeaks/blob/main/README.md
- default SEACR FDR threshold 1 https://github.com/FredHutch/SEACR/blob/master/README.md
#default values\nquality_thresholds: \"0.1, 0.05, 0.01\"\n
Additional reference files may be added to the pipeline, if other species were to be used.
The absolute file paths which must be included are:
- fa: \"/path/to/species.fa\"
- blacklist: \"/path/to/blacklistbed/species.bed\"
The following information must be included:
- regions: \"list of regions to be included; IE chr1 chr2 chr3\"
- macs2_g: \"macs2 genome shorthand; IE mm IE hs\"
There are two manifests, one which required for all pipeliens and one that is only required if running a differential analysis. These files describe information on the samples and desired contrasts. The paths of these files are defined in the snakemake_config.yaml file. These files are:
- samplemanifest
- contrasts
This manifest will include information to sample level information. It includes the following column headers:
- sampleName: the sample name WITHOUT replicate number (IE \"SAMPLE\")
- replicateNumber: the sample replicate number (IE \"1\")
- isControl: whether the sample should be identified as a control (IE \"Y\")
- controlName: the name of the control to use for this sample (IE \"CONTROL\")
- controlReplicateNumber: the replicate number of the control to use for this sample (IE \"1\")
- path_to_R1: the full path to R1 fastq file (IE \"/path/to/sample1.R1.fastq\")
- path_to_R2: the full path to R1 fastq file (IE \"/path/to/sample2.R2.fastq\")
An example sampleManifest file is shown below:
sampleName replicateNumber isControl controlName controlReplicateNumber path_to_R1 path_to_R2 53_H3K4me3 1 N HN6_IgG_rabbit_negative_control 1 PIPELINE_HOME/.test/53_H3K4me3_1.R1.fastq.gz PIPELINE_HOME/.test/53_H3K4me3_1.R2.fastq.gz 53_H3K4me3 2 N HN6_IgG_rabbit_negative_control 1 PIPELINE_HOME/.test/53_H3K4me3_2.R1.fastq.gz PIPELINE_HOME/.test/53_H3K4me3_2.R2.fastq.gz HN6_H3K4me3 1 N HN6_IgG_rabbit_negative_control 1 PIPELINE_HOME/.test/HN6_H3K4me3_1.R1.fastq.gz PIPELINE_HOME/.test/HN6_H3K4me3_1.R2.fastq.gz HN6_H3K4me3 2 N HN6_IgG_rabbit_negative_control 1 PIPELINE_HOME/.test/HN6_H3K4me3_2.R1.fastq.gz PIPELINE_HOME/.test/HN6_H3K4me3_2.R2.fastq.gz HN6_IgG_rabbit_negative_control 1 Y - - PIPELINE_HOME/.test/HN6_IgG_rabbit_negative_control_1.R1.fastq.gz PIPELINE_HOME/.test/HN6_IgG_rabbit_negative_control_1.R2.fastq.gz"},{"location":"user-guide/preparing-files/#222-contrast-manifest-optional","title":"2.2.2 Contrast Manifest (OPTIONAL)","text":"This manifest will include sample information to performed differential comparisons.
An example contrast file:
condition1 condition2 MOC1_siSmyd3_2m_25_HCHO MOC1_siNC_2m_25_HCHO"},{"location":"user-guide/run/","title":"3. Running the Pipeline","text":""},{"location":"user-guide/run/#31-pipeline-overview","title":"3.1 Pipeline Overview","text":"The Snakemake workflow has a multiple options:
Usage: bash ./data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle -m/--runmode=<RUNMODE> -w/--workdir=<WORKDIR>\n1. RUNMODE: [Type: String] Valid options:\n *) init : initialize workdir\n *) run : run with slurm\n *) reset : DELETE workdir dir and re-init it\n *) dryrun : dry run snakemake to generate DAG\n *) unlock : unlock workdir if locked by snakemake\n *) runlocal : run without submitting to sbatch\n *) runtest: run on cluster with included test dataset\n2. WORKDIR: [Type: String]: Absolute or relative path to the output folder with write permissions.\nThe following explains each of the command options:
- Preparation Commands
- init (REQUIRED): This must be performed before any Snakemake run (dry, local, cluster) can be performed. This will copy the necessary config, manifest and Snakefiles needed to run the pipeline to the provided output directory.
- the -f/--force flag can be used in order to re-initialize a workdir that has already been created
- dryrun (OPTIONAL): This is an optional step, to be performed before any Snakemake run (local, cluster). This will check for errors within the pipeline, and ensure that you have read/write access to the files needed to run the full pipeline.
- init (REQUIRED): This must be performed before any Snakemake run (dry, local, cluster) can be performed. This will copy the necessary config, manifest and Snakefiles needed to run the pipeline to the provided output directory.
- Processing Commands
- local: This will run the pipeline on a local node. NOTE: This should only be performed on an interactive node.
- run: This will submit a master job to the cluster, and subsequent sub-jobs as needed to complete the workflow. An email will be sent when the pipeline begins, if there are any errors, and when it completes.
- Other Commands (All optional)
- unlock: This will unlock the pipeline if an error caused it to stop in the middle of a run.
- runtest: This will run a test of the pipeline with test data
To run any of these commands, follow the the syntax:
bash ./data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle --runmode=COMMAND --workdir=/path/to/output/dir\nA typical command workflow, running on the cluser, is as follows:
bash ./data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle --runmode=init --workdir=/path/to/output/dir\n\nbash ./data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle --runmode=dryrun --workdir=/path/to/output/dir\n\nbash ./data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle --runmode=run --workdir=/path/to/output/dir\nWelcome to the CARLISLE Pipeline Tutorial!
"},{"location":"user-guide/test-info/#51-getting-started","title":"5.1 Getting Started","text":"Review the information on the Getting Started for a complete overview the pipeline. The tutorial below will use test data available on NIH Biowulf HPC only. All example code will assume you are running v1.0 of the pipeline, using test data available on GitHub.
A. Change working directory to the CARLISLE repository
B. Initialize Pipeline
bash ./path/to/dir/carlisle --runmode=init --workdir=/path/to/output/dir\nTest data is included in the .test directory as well as the config directory.
A Run the test command to prepare the data, perform a dry-run and submit to the cluster
bash ./path/to/dir/carlisle --runmode=runtest --workdir=/path/to/output/dir\n- An expected output for the
runtestis as follows:Job stats:\njob count min threads max threads\n----------------------------- ------- ------------- -------------\nDESeq 24 1 1\nalign 9 56 56\nalignstats 9 2 2\nall 1 1 1\nbam2bg 9 4 4\ncreate_contrast_data_files 24 1 1\ncreate_contrast_peakcaller_files 12 1 1\ncreate_reference 1 32 32\ncreate_replicate_sample_table 1 1 1\ndiffbb 24 1 1\nfilter 18 2 2\nfindMotif 96 6 6\ngather_alignstats 1 1 1\ngo_enrichment 12 1 1\ngopeaks_broad 16 2 2\ngopeaks_narrow 16 2 2\nmacs2_broad 16 2 2\nmacs2_narrow 16 2 2\nmake_counts_matrix 24 1 1\nmultiqc 2 1 1\nqc_fastqc 9 1 1\nrose 96 2 2\nseacr_relaxed 16 2 2\nseacr_stringent 16 2 2\nspikein_assessment 1 1 1\ntrim 9 56 56\ntotal 478 1 56\n
Review the expected outputs on the Output page. If there are errors, review and performing stesp described on the Troubleshooting page as needed.
"},{"location":"user-guide/troubleshooting/","title":"Troubleshooting","text":"Recommended steps to troubleshoot the pipeline.
"},{"location":"user-guide/troubleshooting/#11-email","title":"1.1 Email","text":"Check your email for an email regarding pipeline failure. You will receive an email from slurm@biowulf.nih.gov with the subject: Slurm Job_id=[#] Name=CARLISLE Failed, Run time [time], FAILED, ExitCode 1
"},{"location":"user-guide/troubleshooting/#12-review-the-log-files","title":"1.2 Review the log files","text":"Review the logs in two ways:
- Review the master slurm file: This file will be found in the
/path/to/results/dir/and titledslurm-[jobid].out. Reviewing this file will tell you what rule errored, and for any local SLURM jobs, provide error details - Review the individual rule log files: After reviewing the master slurm-file, review the specific rules that failed within the
/path/to/results/dir/logs/. Each rule will include a.errand.outfile, with the following formatting:{rulename}.{masterjobID}.{individualruleID}.{wildcards from the rule}.{out or err}
After addressing the issue, unlock the output directory, perform another dry-run and check the status of the pipeline, then resubmit to the cluster.
#unlock dir\nbash ./data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle --runmode=unlock --workdir=/path/to/output/dir\n\n#perform dry-run\nbash ./data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle --runmode=dryrun --workdir=/path/to/output/dir\n\n#submit to cluster\nbash ./data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle --runmode=run --workdir=/path/to/output/dir\nIf after troubleshooting, the error cannot be resolved, or if a bug is found, please create an issue and send and email to Samantha Chill.
"}]} \ No newline at end of file diff --git a/sitemap.xml b/sitemap.xml new file mode 100644 index 0000000..0f8724e --- /dev/null +++ b/sitemap.xml @@ -0,0 +1,3 @@ + +Contributions¶
The following members contributed to the development of the CARLISLE pipeline:
- Samantha Sevilla
- Vishal Koparde
- Hsien-chao Chou
- Sohyoung Kim
- Yue Hu
- Vassiliki Saloura
VK, SS, SK, HC contributed to the generating the source code and all members contributed to the main concepts and analysis.
Last update: 2024-02-21
Overview¶
The CARLISLE github repository is stored locally, and will be used for project deployment. Multiple projects can be deployed from this one point simultaneously, without concern.
1. Getting Started¶
1.1 Introduction¶
The CARLISLE Pipelie beings with raw FASTQ files and performs trimming followed by alignment using BOWTIE2. Data is then normalized through either the use of an user-species species (IE E.Coli) spike-in control or through the determined library size. Peaks are then called using MACS2, SEACR, and GoPEAKS with various options selected by the user. Peaks are then annotated, and summarized into reports. If designated, differential analysis is performed using DESEQ2. QC reports are also generated with each project using FASTQC and MULTIQC. Annotations are added using HOMER and ROSE. GSEA Enrichment analysis predictions are added using CHIPENRICH.
The following are sub-commands used within CARLISLE:
- initialize: initalize the pipeline
- dryrun: predict the binding of peptides to any MHC molecule
- cluster: execute the pipeline on the Biowulf HPC
- local: execute a local, interactive, session
- git: execute GitHub actions
- unlock: unlock directory
- DAG: create DAG report
- report: create SNAKEMAKE report
- runtest: copies test manifests and files to WORKDIR
1.2 Setup Dependencies¶
CARLISLE has several dependencies listed below. These dependencies can be installed by a sysadmin. All dependencies will be automatically loaded if running from Biowulf.
- bedtools: "bedtools/2.30.0"
- bedops: "bedops/2.4.40"
- bowtie2: "bowtie/2-2.4.2"
- cutadapt: "cutadapt/1.18"
- fastqc: "fastqc/0.11.9"
- fastq_screen: "fastq_screen/0.15.2"
- fastq_val: "/data/CCBR_Pipeliner/iCLIP/bin/fastQValidator"
- fastxtoolkit: "fastxtoolkit/0.0.14"
- gopeaks: "github clone https://github.com/maxsonBraunLab/gopeaks"
- macs2: "macs/2.2.7.1"
- multiqc: "multiqc/1.9"
- perl: "perl/5.34.0"
- picard: "picard/2.26.9"
- python37: "python/3.7"
- R: "R/4.2.2"
- rose: "ROSE/1.3.1"
- samtools: "samtools/1.15"
- seacr: "seacr/1.4-beta.2"
- ucsc: "ucsc/407"
1.3 Login to the cluster¶
CARLISLE has been exclusively tested on Biowulf HPC. Login to the cluster's head node and move into the pipeline location.
# ssh into cluster's head node
+ssh -Y $USER@biowulf.nih.gov
+1.4 Load an interactive session¶
An interactive session should be started before performing any of the pipeline sub-commands, even if the pipeline is to be executed on the cluster.
# Grab an interactive node
+sinteractive --time=12:00:00 --mem=8gb --cpus-per-task=4 --pty bash
+ Last update: 2024-02-21
4. Expected Outputs¶
The following directories are created under the WORKDIR/results directory:
- alignment_stats: this directory include information on the alignment of each sample
- bam: this directory includes BAM files, statistics on samples, statistics on spike-in controls for each sample
- bedgraph: this directory includes BEDGRAPH files and statistic summaries for each sample
- bigwig: this directory includes the bigwig files for each sample
- peaks: this directory contains a sub-directory that relates to the quality threshold used.
- quality threshold
- contrasts: this directory includes the contrasts for each line listed in the contrast manifest
- peak_caller: this directory includes all peak calls from each peak_caller (SEACR, MACS2, GOPEAKS) for each sample
- annotation
- go_enrichment: this directory includes gene set enrichment pathway predictions
- homer: this directory includes the annotation output from HOMER
- rose: this directory includes the annotation output from ROSE
- annotation
- quality threshold
- qc: this directory includes MULTIQC reports and spike-in control reports (when applicable)
├── alignment_stats
+├── bam
+├── bedgraph
+├── bigwig
+├── fragments
+├── peaks
+│ ├── 0.05
+│ │ ├── contrasts
+│ │ │ ├── contrast_id1.dedup_status
+│ │ │ └── contrast_id2.dedup_status
+│ │ ├── gopeaks
+│ │ │ ├── annotation
+│ │ │ │ ├── go_enrichment
+│ │ │ │ │ ├── contrast_id1.dedup_status.go_enrichment_tables
+│ │ │ │ │ └── contrast_id2.dedup_status.go_enrichment_html_report
+│ │ │ │ ├── homer
+│ │ │ │ │ ├── replicate_id1_vs_control_id.dedup_status.gopeaks_broad.motifs
+│ │ │ │ │ │ ├── homerResults
+│ │ │ │ │ │ └── knownResults
+│ │ │ │ │ ├── replicate_id1_vs_control_id.dedup_status.gopeaks_narrow.motifs
+│ │ │ │ │ │ ├── homerResults
+│ │ │ │ │ │ └── knownResults
+│ │ │ │ │ ├── replicate_id2_vs_control_id.dedup_status.gopeaks_broad.motifs
+│ │ │ │ │ │ ├── homerResults
+│ │ │ │ │ │ └── knownResults
+│ │ │ │ │ ├── replicate_id2_vs_control_id.dedup_status.gopeaks_narrow.motifs
+│ │ │ │ │ │ ├── homerResults
+│ │ │ │ │ │ └── knownResults
+│ │ │ │ └── rose
+│ │ │ │ ├── replicate_id1_vs_control_id.dedup_status.gopeaks_broad.12500
+│ │ │ │ ├── replicate_id1_vs_control_id.dedup_status.gopeaks_narrow.12500
+│ │ │ │ ├── replicate_id2_vs_control_id.dedup_status.dedup.gopeaks_broad.12500
+│ │ │ │ ├── replicate_id2_vs_control_id.dedup_status.dedup.gopeaks_narrow.12500
+│ │ │ └── peak_output
+│ │ ├── macs2
+│ │ │ ├── annotation
+│ │ │ │ ├── go_enrichment
+│ │ │ │ │ ├── contrast_id1.dedup_status.go_enrichment_tables
+│ │ │ │ │ └── contrast_id2.dedup_status.go_enrichment_html_report
+│ │ │ │ ├── homer
+│ │ │ │ │ ├── replicate_id1_vs_control_id.dedup_status.macs2_narrow.motifs
+│ │ │ │ │ │ ├── homerResults
+│ │ │ │ │ │ └── knownResults
+│ │ │ │ │ ├── replicate_id1_vs_control_id.dedup_status.macs2_broad.motifs
+│ │ │ │ │ │ ├── homerResults
+│ │ │ │ │ │ └── knownResults
+│ │ │ │ │ ├── replicate_id2_vs_control_id.dedup_status.macs2_narrow.motifs
+│ │ │ │ │ │ ├── homerResults
+│ │ │ │ │ │ └── knownResults
+│ │ │ │ │ ├── replicate_id2_vs_control_id.dedup_status.macs2_broad.motifs
+│ │ │ │ │ │ ├── homerResults
+│ │ │ │ │ │ └── knownResults
+│ │ │ │ └── rose
+│ │ │ │ ├── replicate_id1_vs_control_id.dedup_status.macs2_broad.12500
+│ │ │ │ ├── replicate_id1_vs_control_id.dedup_status.macs2_narrow.12500
+│ │ │ │ ├── replicate_id2_vs_control_id.dedup_status.macs2_broad.12500
+│ │ │ │ ├── replicate_id2_vs_control_id.dedup_status.macs2_narrow.12500
+│ │ │ └── peak_output
+│ │ └── seacr
+│ │ │ ├── annotation
+│ │ │ │ ├── go_enrichment
+│ │ │ │ │ ├── contrast_id1.dedup_status.go_enrichment_tables
+│ │ │ │ │ └── contrast_id2.dedup_status.go_enrichment_html_report
+│ │ │ │ ├── homer
+│ │ │ │ │ ├── replicate_id1_vs_control_id.dedup_status.seacr_non_relaxed.motifs
+│ │ │ │ │ │ ├── homerResults
+│ │ │ │ │ │ └── knownResults
+│ │ │ │ │ ├── replicate_id1_vs_control_id.dedup_status.seacr_non_stringent.motifs
+│ │ │ │ │ │ ├── homerResults
+│ │ │ │ │ │ └── knownResults
+│ │ │ │ │ ├── replicate_id1_vs_control_id.dedup_status.seacr_norm_relaxed.motifs
+│ │ │ │ │ │ ├── homerResults
+│ │ │ │ │ │ └── knownResults
+│ │ │ │ │ ├── replicate_id1_vs_control_id.dedup_status.seacr_norm_stringent.motifs
+│ │ │ │ │ │ ├── homerResults
+│ │ │ │ │ │ └── knownResults
+│ │ │ │ │ ├── replicate_id2_vs_control_id.dedup_status.seacr_non_relaxed.motifs
+│ │ │ │ │ │ ├── homerResults
+│ │ │ │ │ │ └── knownResults
+│ │ │ │ │ ├── replicate_id2_vs_control_id.dedup_status.seacr_non_stringent.motifs
+│ │ │ │ │ │ ├── homerResults
+│ │ │ │ │ │ └── knownResults
+│ │ │ │ │ ├── replicate_id2_vs_control_id.dedup_status.seacr_norm_relaxed.motifs
+│ │ │ │ │ │ ├── homerResults
+│ │ │ │ │ │ └── knownResults
+│ │ │ │ │ ├── replicate_id2_vs_control_id.dedup_status.seacr_norm_stringent.motifs
+│ │ │ │ │ │ ├── homerResults
+│ │ │ │ │ │ └── knownResults
+│ │ │ │ └── rose
+│ │ │ │ ├── replicate_id1_vs_control_id.dedup_status.seacr_non_relaxed.12500
+│ │ │ │ ├── replicate_id1_vs_control_id.dedup_status.seacr_non_stringent.12500
+│ │ │ │ ├── replicate_id1_vs_control_id.dedup_status.seacr_norm_relaxed.12500
+│ │ │ │ ├── replicate_id1_vs_control_id.dedup_status.seacr_norm_stringent.12500
+│ │ │ │ ├── replicate_id2_vs_control_id.dedup_status.seacr_non_relaxed.12500
+│ │ │ │ ├── replicate_id2_vs_control_id.dedup_status.seacr_non_stringent.12500
+│ │ │ │ ├── replicate_id2_vs_control_id.dedup_status.seacr_norm_relaxed.12500
+│ │ │ │ ├── replicate_id2_vs_control_id.dedup_status.seacr_norm_stringent.12500
+│ │ └── peak_output
+└── qc
+ ├── fastqc_raw
+ └── fqscreen_raw
+ Last update: 2024-02-21
2. Preparing Files¶
The pipeline is controlled through editing configuration and manifest files. Defaults are found in the /WORKDIR/config and /WORKDIR/manifest directories, after initialization.
2.1 Configs¶
The configuration files control parameters and software of the pipeline. These files are listed below:
- config/config.yaml
- resources/cluster.yaml
- resources/tools.yaml
2.1.1 Cluster Config¶
The cluster configuration file dictates the resouces to be used during submission to Biowulf HPC. There are two differnt ways to control these parameters - first, to control the default settings, and second, to create or edit individual rules. These parameters should be edited with caution, after significant testing.
2.1.2 Tools Config¶
The tools configuration file dictates the version of each software or program that is being used in the pipeline.
2.1.3 Config YAML¶
There are several groups of parameters that are editable for the user to control the various aspects of the pipeline. These are :
- Folders and Paths
- These parameters will include the input and ouput files of the pipeline, as well as list all manifest names.
- User parameters
- These parameters will control the pipeline features. These include thresholds and whether to perform processes.
- References
- These parameters will control the location of index files, spike-in references, adaptors and species calling information.
2.1.3.1 User Parameters¶
2.1.3.1.1 (Spike in Controls)¶
The pipeline allows for the use of a species specific spike-in control, or the use of normalization via library size. The parameter spikein_genome should be set to the species term used in spikein_reference.
For example for ecoli spike-in:
run_contrasts: "Y"
+norm_method: "spikein"
+spikein_genome: "ecoli"
+spikein_reference:
+ ecoli:
+ fa: "PIPELINE_HOME/resources/spikein/Ecoli_GCF_000005845.2_ASM584v2_genomic.fna"
+For example for drosophila spike-in:
run_contrasts: "Y"
+norm_method: "spikein"
+spikein_genome: "drosophila"
+spikein_reference:
+ drosophila:
+ fa: "/fdb/igenomes/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
+If it's determined that the amount of spike-in is not sufficient for the run, a library normaliaztion can be performed. 1. Complete a CARLISLE run with spike-in set to "Y". This will allow for the complete assessment of the spike-in. 2. Run inital QC analysis on the output data 3. Add the alignment_stats dir to the configuration file. 4. Re-run the CARLISLE pipeline
2.1.3.1.2 Duplication Status¶
Users can select duplicated peaks (dedup) or non-deduplicated peaks (no_dedup) through the user parameter.
dupstatus: "dedup, no_dedup"
+2.1.3.1.3 Peak Caller¶
Three peak callers are available for deployment within the pipeline, with different settings deployed for each caller.
- MACS2 is available with two peak calling options: narrowPeak or broadPeak. NOTE: DESeq step generally fails for broadPeak; generally has too many calls.
peaktype: "macs2_narrow, macs2_broad," + - SEACR is available with four peak calling options: stringent or relaxed parameters, to be paired with "norm" for samples without a spike-in control and "non" for samples with a spikein control
peaktype: "seacr_stringent, seacr_relaxed" + - GOPEAKS is available with two peak calling options: narrowpeaks or broadpeaks A complete list of the available peak calling parameters and the recommended list of parameters is provided below:
peaktype: "gopeaks_narrow, gopeaks_broad" +
| Peak Caller | Narrow | Broad | Normalized, Stringent | Normalized, Relaxed | Non-Normalized, Stringent | Non-Normalized, Relaxed |
|---|---|---|---|---|---|---|
| Macs2 | AVAIL | AVAIL | NA | NA | NA | NA |
| SEACR | NA | NA | AVAIL w/o SPIKEIN | AVAIL w/o SPIKEIN | AVAIL w/ SPIKEIN | AVAIL w/ SPIKEIN |
| GoPeaks | AVAIL | AVAIL | NA | NA | NA | NA |
# Recommended list
+### peaktype: "macs2_narrow, macs2_broad, gopeaks_narrow, gopeaks_broad"
+
+# Available list
+### peaktype: "macs2_narrow, macs2_broad, seacr_norm_stringent, seacr_norm_relaxed, seacr_non_stringent, seacr_non_relaxed, gopeaks_narrow, gopeaks_broad"
+2.1.3.1.3.1 Macs2 additional option¶
MACS2 can be run with or without the control. adding a control will increase peak specificity Selecting "Y" for the macs2_control will run the paired control sample provided in the sample manifest
2.1.3.1.4 Quality Tresholds¶
Thresholds for quality can be controled through the quality_tresholds parameter. This must be a list of comma separated values. minimum of numeric value required.
- default MACS2 qvalue is 0.05 https://manpages.ubuntu.com/manpages/xenial/man1/macs2_callpeak.1.html
- default GOPEAKS pvalue is 0.05 https://github.com/maxsonBraunLab/gopeaks/blob/main/README.md
- default SEACR FDR threshold 1 https://github.com/FredHutch/SEACR/blob/master/README.md
#default values +quality_thresholds: "0.1, 0.05, 0.01" +
2.1.3.2 References¶
Additional reference files may be added to the pipeline, if other species were to be used.
The absolute file paths which must be included are:
- fa: "/path/to/species.fa"
- blacklist: "/path/to/blacklistbed/species.bed"
The following information must be included:
- regions: "list of regions to be included; IE chr1 chr2 chr3"
- macs2_g: "macs2 genome shorthand; IE mm IE hs"
2.2 Preparing Manifests¶
There are two manifests, one which required for all pipeliens and one that is only required if running a differential analysis. These files describe information on the samples and desired contrasts. The paths of these files are defined in the snakemake_config.yaml file. These files are:
- samplemanifest
- contrasts
2.2.1 Samples Manifest (REQUIRED)¶
This manifest will include information to sample level information. It includes the following column headers:
- sampleName: the sample name WITHOUT replicate number (IE "SAMPLE")
- replicateNumber: the sample replicate number (IE "1")
- isControl: whether the sample should be identified as a control (IE "Y")
- controlName: the name of the control to use for this sample (IE "CONTROL")
- controlReplicateNumber: the replicate number of the control to use for this sample (IE "1")
- path_to_R1: the full path to R1 fastq file (IE "/path/to/sample1.R1.fastq")
- path_to_R2: the full path to R1 fastq file (IE "/path/to/sample2.R2.fastq")
An example sampleManifest file is shown below:
| sampleName | replicateNumber | isControl | controlName | controlReplicateNumber | path_to_R1 | path_to_R2 |
|---|---|---|---|---|---|---|
| 53_H3K4me3 | 1 | N | HN6_IgG_rabbit_negative_control | 1 | PIPELINE_HOME/.test/53_H3K4me3_1.R1.fastq.gz | PIPELINE_HOME/.test/53_H3K4me3_1.R2.fastq.gz |
| 53_H3K4me3 | 2 | N | HN6_IgG_rabbit_negative_control | 1 | PIPELINE_HOME/.test/53_H3K4me3_2.R1.fastq.gz | PIPELINE_HOME/.test/53_H3K4me3_2.R2.fastq.gz |
| HN6_H3K4me3 | 1 | N | HN6_IgG_rabbit_negative_control | 1 | PIPELINE_HOME/.test/HN6_H3K4me3_1.R1.fastq.gz | PIPELINE_HOME/.test/HN6_H3K4me3_1.R2.fastq.gz |
| HN6_H3K4me3 | 2 | N | HN6_IgG_rabbit_negative_control | 1 | PIPELINE_HOME/.test/HN6_H3K4me3_2.R1.fastq.gz | PIPELINE_HOME/.test/HN6_H3K4me3_2.R2.fastq.gz |
| HN6_IgG_rabbit_negative_control | 1 | Y | - | - | PIPELINE_HOME/.test/HN6_IgG_rabbit_negative_control_1.R1.fastq.gz | PIPELINE_HOME/.test/HN6_IgG_rabbit_negative_control_1.R2.fastq.gz |
2.2.2 Contrast Manifest (OPTIONAL)¶
This manifest will include sample information to performed differential comparisons.
An example contrast file:
| condition1 | condition2 |
|---|---|
| MOC1_siSmyd3_2m_25_HCHO | MOC1_siNC_2m_25_HCHO |
Last update: 2024-02-21
3. Running the Pipeline¶
3.1 Pipeline Overview¶
The Snakemake workflow has a multiple options:
Usage: bash ./data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle -m/--runmode=<RUNMODE> -w/--workdir=<WORKDIR>
+1. RUNMODE: [Type: String] Valid options:
+ *) init : initialize workdir
+ *) run : run with slurm
+ *) reset : DELETE workdir dir and re-init it
+ *) dryrun : dry run snakemake to generate DAG
+ *) unlock : unlock workdir if locked by snakemake
+ *) runlocal : run without submitting to sbatch
+ *) runtest: run on cluster with included test dataset
+2. WORKDIR: [Type: String]: Absolute or relative path to the output folder with write permissions.
+3.2 Commands explained¶
The following explains each of the command options:
- Preparation Commands
- init (REQUIRED): This must be performed before any Snakemake run (dry, local, cluster) can be performed. This will copy the necessary config, manifest and Snakefiles needed to run the pipeline to the provided output directory.
- the -f/--force flag can be used in order to re-initialize a workdir that has already been created
- dryrun (OPTIONAL): This is an optional step, to be performed before any Snakemake run (local, cluster). This will check for errors within the pipeline, and ensure that you have read/write access to the files needed to run the full pipeline.
- init (REQUIRED): This must be performed before any Snakemake run (dry, local, cluster) can be performed. This will copy the necessary config, manifest and Snakefiles needed to run the pipeline to the provided output directory.
- Processing Commands
- local: This will run the pipeline on a local node. NOTE: This should only be performed on an interactive node.
- run: This will submit a master job to the cluster, and subsequent sub-jobs as needed to complete the workflow. An email will be sent when the pipeline begins, if there are any errors, and when it completes.
- Other Commands (All optional)
- unlock: This will unlock the pipeline if an error caused it to stop in the middle of a run.
- runtest: This will run a test of the pipeline with test data
To run any of these commands, follow the the syntax:
bash ./data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle --runmode=COMMAND --workdir=/path/to/output/dir
+3.3 Typical Workflow¶
A typical command workflow, running on the cluser, is as follows:
bash ./data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle --runmode=init --workdir=/path/to/output/dir
+
+bash ./data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle --runmode=dryrun --workdir=/path/to/output/dir
+
+bash ./data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle --runmode=run --workdir=/path/to/output/dir
+ Last update: 2024-02-21
5. Pipeline Tutorial¶
Welcome to the CARLISLE Pipeline Tutorial!
5.1 Getting Started¶
Review the information on the Getting Started for a complete overview the pipeline. The tutorial below will use test data available on NIH Biowulf HPC only. All example code will assume you are running v1.0 of the pipeline, using test data available on GitHub.
A. Change working directory to the CARLISLE repository
B. Initialize Pipeline
bash ./path/to/dir/carlisle --runmode=init --workdir=/path/to/output/dir
+5.2 Submit the test data¶
Test data is included in the .test directory as well as the config directory.
A Run the test command to prepare the data, perform a dry-run and submit to the cluster
bash ./path/to/dir/carlisle --runmode=runtest --workdir=/path/to/output/dir
+- An expected output for the
runtestis as follows:Job stats: +job count min threads max threads +----------------------------- ------- ------------- ------------- +DESeq 24 1 1 +align 9 56 56 +alignstats 9 2 2 +all 1 1 1 +bam2bg 9 4 4 +create_contrast_data_files 24 1 1 +create_contrast_peakcaller_files 12 1 1 +create_reference 1 32 32 +create_replicate_sample_table 1 1 1 +diffbb 24 1 1 +filter 18 2 2 +findMotif 96 6 6 +gather_alignstats 1 1 1 +go_enrichment 12 1 1 +gopeaks_broad 16 2 2 +gopeaks_narrow 16 2 2 +macs2_broad 16 2 2 +macs2_narrow 16 2 2 +make_counts_matrix 24 1 1 +multiqc 2 1 1 +qc_fastqc 9 1 1 +rose 96 2 2 +seacr_relaxed 16 2 2 +seacr_stringent 16 2 2 +spikein_assessment 1 1 1 +trim 9 56 56 +total 478 1 56 +
5.3 Review outputs¶
Review the expected outputs on the Output page. If there are errors, review and performing stesp described on the Troubleshooting page as needed.
Last update: 2024-02-21
Troubleshooting¶
Recommended steps to troubleshoot the pipeline.
1.1 Email¶
Check your email for an email regarding pipeline failure. You will receive an email from slurm@biowulf.nih.gov with the subject: Slurm Job_id=[#] Name=CARLISLE Failed, Run time [time], FAILED, ExitCode 1
1.2 Review the log files¶
Review the logs in two ways:
- Review the master slurm file: This file will be found in the
/path/to/results/dir/and titledslurm-[jobid].out. Reviewing this file will tell you what rule errored, and for any local SLURM jobs, provide error details - Review the individual rule log files: After reviewing the master slurm-file, review the specific rules that failed within the
/path/to/results/dir/logs/. Each rule will include a.errand.outfile, with the following formatting:{rulename}.{masterjobID}.{individualruleID}.{wildcards from the rule}.{out or err}
1.3 Restart the run¶
After addressing the issue, unlock the output directory, perform another dry-run and check the status of the pipeline, then resubmit to the cluster.
#unlock dir
+bash ./data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle --runmode=unlock --workdir=/path/to/output/dir
+
+#perform dry-run
+bash ./data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle --runmode=dryrun --workdir=/path/to/output/dir
+
+#submit to cluster
+bash ./data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle --runmode=run --workdir=/path/to/output/dir
+1.4 Contact information¶
If after troubleshooting, the error cannot be resolved, or if a bug is found, please create an issue and send and email to Samantha Chill.
Last update: 2024-02-21