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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,30 +1,35 @@ | ||
| # 12/16/22 | ||
| ################################################ | ||
| # CHANGELOG | ||
| ### samples retired 2/6/24 | ||
| <!-- VS589.R1.fastq.gz,HN6_H3K4me3_2.R1.fastq.gz | ||
| VS589.R2.fastq.gz,HN6_H3K4me3_2.R2.fastq.gz | ||
| VS594.R1.fastq.gz,HN6_H4K20me3_1.R1.fastq.gz | ||
| VS594.R2.fastq.gz,HN6_H4K20me3_1.R2.fastq.gz | ||
| VS595.R1.fastq.gz,HN6_H4K20me3_2.R1.fastq.gz | ||
| VS595.R2.fastq.gz,HN6_H4K20me3_2.R2.fastq.gz | ||
| VS597.R1.fastq.gz,53_H4K20m3_1.R1.fastq.gz | ||
| VS597.R2.fastq.gz,53_H4K20m3_1.R2.fastq.gz | ||
| VS598.R1.fastq.gz,53_H4K20m3_2.R1.fastq.gz --> | ||
| ### 12/16/22 | ||
| New test data is added to pipeline | ||
|
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| ################################################ | ||
| # HG38 | ||
| # sample location | ||
| /data/CCBR/projects/ccbr1155/CS031014/fastq | ||
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| # sample ids mapping; original to renamed | ||
| VS586.R1.fastq.gz,HN6_IgG_rabbit_negative_control_1.R1.fastq.gz | ||
| VS586.R2.fastq.gz,HN6_IgG_rabbit_negative_control_1.R2.fastq.gz | ||
| VS588.R1.fastq.gz,HN6_H3K4me3_1.R1.fastq.gz | ||
| VS588.R2.fastq.gz,HN6_H3K4me3_1.R2.fastq.gz | ||
| VS589.R1.fastq.gz,HN6_H3K4me3_2.R1.fastq.gz | ||
| VS589.R2.fastq.gz,HN6_H3K4me3_2.R2.fastq.gz | ||
| VS591.R1.fastq.gz,53_H3K4me3_1.R1.fastq.gz | ||
| VS591.R2.fastq.gz,53_H3K4me3_1.R2.fastq.gz | ||
| VS592.R1.fastq.gz,53_H3K4me3_2.R1.fastq.gz | ||
| VS592.R2.fastq.gz,53_H3K4me3_2.R2.fastq.gz | ||
| VS594.R1.fastq.gz,HN6_H4K20me3_1.R1.fastq.gz | ||
| VS594.R2.fastq.gz,HN6_H4K20me3_1.R2.fastq.gz | ||
| VS595.R1.fastq.gz,HN6_H4K20me3_2.R1.fastq.gz | ||
| VS595.R2.fastq.gz,HN6_H4K20me3_2.R2.fastq.gz | ||
| VS597.R1.fastq.gz,53_H4K20m3_1.R1.fastq.gz | ||
| VS597.R2.fastq.gz,53_H4K20m3_1.R2.fastq.gz | ||
| VS598.R1.fastq.gz,53_H4K20m3_2.R1.fastq.gz | ||
| VS588.R1.fastq.gz,HN6_H3K4me3_1.R1.fastq.gz | ||
| VS588.R2.fastq.gz,HN6_H3K4me3_1.R2.fastq.gz | ||
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| # subset each of the samples | ||
| fq_original_loc="/data/CCBR/projects/ccbr1155/CS031014/fastq";\ | ||
| test_loc="/data/CCBR_Pipeliner/Pipelines/CARLISLE_dev/.test";\ | ||
| fq_list=("HN6_IgG_rabbit_negative_control_1.R1.fastq.gz" "HN6_IgG_rabbit_negative_control_1.R2.fastq.gz" "HN6_H3K4me3_1.R1.fastq.gz" "HN6_H3K4me3_1.R2.fastq.gz" "HN6_H3K4me3_2.R1.fastq.gz" "HN6_H3K4me3_2.R2.fastq.gz" "53_H3K4me3_1.R1.fastq.gz" "53_H3K4me3_1.R2.fastq.gz" "53_H3K4me3_2.R1.fastq.gz" "53_H3K4me3_2.R2.fastq.gz" "HN6_H4K20me3_1.R1.fastq.gz" "HN6_H4K20me3_1.R2.fastq.gz" "HN6_H4K20me3_2.R1.fastq.gz" "HN6_H4K20me3_2.R2.fastq.gz" "53_H4K20m3_1.R1.fastq.gz" "53_H4K20m3_1.R2.fastq.gz" "53_H4K20m3_2.R1.fastq.gz" "53_H4K20m3_2.R2.fastq.gz");\ | ||
| for fq in ${fq_list[@]}; do echo $fq; remove_ext=`echo $fq | sed "s/.gz//g"`; zcat $fq_original_loc/$fq | head -1000000 > $test_loc/$remove_ext; gzip $test_loc/$remove_ext; done | ||
| for fq in ${fq_list[@]}; do echo $fq; remove_ext=`echo $fq | sed "s/.gz//g"`; zcat $fq_original_loc/$fq | head -1000000 > $test_loc/$remove_ext; gzip $test_loc/$remove_ext; done |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,2 @@ | ||
| condition1 condition2 | ||
| 53_H3K4me3 HN6_H3K4me3 | ||
| 53_H4K20m3 HN6_H4K20me3 | ||
| 53_H3K4me3 HN6_H3K4me3 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,65 @@ | ||
| ## CARLISLE development version | ||
| - Refactors R packages to a common source location (#118, @slsevilla) | ||
| - Adds a --force flag to allow for re-initialization of a workdir (#97, @slsevilla) | ||
| - Fixes error with testrun in DESEQ2 (#113, @slsevilla) | ||
| - Decreases the number of samples being run with testrun, essentially running tinytest as default and removing tinytest as an option (#115, @slsevilla) | ||
| - Reads version from VERSION file instead of github repo link (#96, #112, @slsevilla) | ||
| - Added a CHANGELOG (#116, @slsevilla) | ||
| - Fix: RNA report bug, caused by hard-coding of PC1-3, when only PC1-2 were generated (#104, @slsevilla) | ||
| - Minor documentation improvements. (#100, @kelly-sovacool) | ||
| - Fix: allow printing the version or help message even if singularity is not in the path. (#110, @kelly-sovacool) | ||
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| ## CARLISLE v2.4.1 | ||
| - Add GitHub Action to add issues/PRs to personal project boards by @kelly-sovacool in #95 | ||
| - Create install script by @kelly-sovacool in #93 | ||
| - feat: use summits bed for homer input; save temporary files; fix deseq2 bug by @slsevilla in #108 | ||
| - docs: adding citation and DOI to pipeline by @slsevilla in #107 | ||
| - Test a dryrun with GitHub Actions by @kelly-sovacool in #94 | ||
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| ## CARLISLE v2.4.0 | ||
| - Feature- Merged Yue's fork, adding DEEPTOOLS by @slsevilla in #85 | ||
| - Feature- Added tracking features from SPOOK by @slsevilla in #88 | ||
| - Feature - Dev test run completed by @slsevilla in #89 | ||
| - Bug - Fixed bugs related to Biowulf transition | ||
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| ## CARLISLE v2.1.0 | ||
| - enhancement | ||
| - update gopeaks resources | ||
| - change SEACR to run "norm" without spikein controls, "non" with spikein controls | ||
| - update docs for changes; provide extra troubleshooting guidance | ||
| - fix GoEnrich bug for failed plots | ||
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| ## CARLISLE v2.0.1 | ||
| - fix error when contrasts set to "N" | ||
| - adjust goenrich resources to be more efficient | ||
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| ## CARLISLE 2.0.0 | ||
| - Add a MAPQ filter to samtools (rule align) | ||
| - Add GoPeaks MultiQC module | ||
| - Allow for library normalization to occur during first pass | ||
| - Add --broad-cutoff to MACS2 broad peak calling for MACS2 | ||
| - Create a spike in QC report | ||
| - Reorganize file structure to help with qthreshold folder | ||
| - Update variable names of all peak caller | ||
| - Merge rules with input/output/wildcard congruency | ||
| - Convert the "spiked" variable to "norm_method | ||
| - Add name of control used to MACS2 peaks | ||
| - Running extra control:sample comparisons that are not needed | ||
| - improved resource allocation | ||
| - test data originally included 1475 jobs, this version includes 1087 jobs (reduction of 25%) despite including additional features | ||
| - moved ~12% of all jobs to local deployment (within SLURM submission) | ||
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| ## CARLISLE 1.2.0 | ||
| - merge increases to resources; update workflow img, contributions | ||
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| ## CARLISLE 1.1.1 | ||
| - patch for gz bigbed bug | ||
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| ## CARLISLE 1.1.0 | ||
| - add broad-cutoff to macs2 broad peaks param settings | ||
| - add non.stringent and non.relaxed to annotation options | ||
| - merge DESEQ and DESEQ2 rules together | ||
| - identify some files as temp | ||
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| ## CARLISLE 1.0.1 | ||
| - contains patch for DESEQ error with non hs1 reference samples |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,9 @@ | ||
| ## mm10 download | ||
| https://bitbucket.org/young_computation/rose/src/master/annotation/mm10_refseq.ucsc | ||
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| `create_hs1_ucsc.sh` script was used to create the hs1 ucsc file. | ||
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| #### hg19_refseq.ucsc and hg38_refseq.ucsc source | ||
| /data/khanlab3/gb_omics/processed_DATA/YueHu/cutrun_120822# hg19_refseq.ucsc and hg38_refseq.ucsc source | ||
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| # info on these resources is outlined in: https://github.com/CCBR/CARLISLE/issues/27 | ||
| # info on these resources is outlined in: https://github.com/CCBR/CARLISLE/issues/27 |
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