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Update tasks and tools table with Summary_PerCellOutput #1356

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Update tasks and tools table with Summary_PerCellOutput #1356

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921ec55
Update README.md
gsenior09 Aug 7, 2024
09ad600
Updated pipeline_versions.txt with all pipeline version information
actions-user Aug 7, 2024
19167a1
Update website/docs/Pipelines/snM3C/README.md
akovalsk Aug 8, 2024
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66 changes: 33 additions & 33 deletions pipeline_versions.txt
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Original file line number Diff line number Diff line change
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Pipeline Name Version Date of Last Commit
MultiSampleSmartSeq2 2.2.21 2023-04-19
SmartSeq2SingleSample 5.1.20 2023-04-19
snm3C 4.0.0 2024-03-15
Optimus 7.1.0 2024-05-20
Optimus 7.4.0 2024-07-11
Multiome 5.3.1 2024-07-18
PairedTag 1.3.1 2024-07-18
atac 2.2.0 2024-07-11
SlideSeq 3.2.0 2024-07-11
snm3C 4.0.2 2024-07-09
MultiSampleSmartSeq2SingleNucleus 1.4.0 2024-07-11
scATAC 1.3.2 2023-08-03
MultiSampleSmartSeq2SingleNucleus 1.3.4 2024-04-12
SlideSeq 3.1.6 2024-05-20
SmartSeq2SingleSample 5.1.20 2023-04-19
BuildIndices 3.0.0 2023-12-06
PairedTag 0.7.0 2024-05-20
atac 2.0.0 2024-05-20
Multiome 5.0.0 2024-05-20
MultiSampleSmartSeq2 2.2.21 2023-04-19
CEMBA 1.1.6 2023-12-18
BuildCembaReferences 1.0.0 2020-11-15
IlluminaGenotypingArray 1.12.17 2024-03-26
ExomeReprocessing 3.1.19 2024-03-26
WholeGenomeReprocessing 3.1.20 2024-03-26
ExternalExomeReprocessing 3.1.21 2024-03-26
ExternalWholeGenomeReprocessing 2.1.21 2024-03-26
CramToUnmappedBams 1.1.2 2022-04-14
AnnotationFiltration 1.2.5 2023-12-18
BroadInternalUltimaGenomics 1.0.17 2024-03-26
BroadInternalRNAWithUMIs 1.0.29 2024-03-26
BroadInternalImputation 1.1.10 2023-12-18
BroadInternalArrays 1.1.7 2024-03-26
UltimaGenomicsWholeGenomeCramOnly 1.0.16 2024-03-26
UltimaGenomicsWholeGenomeCramOnly 1.0.19 2024-06-12
GDCWholeGenomeSomaticSingleSample 1.3.1 2024-01-19
VariantCalling 2.1.18 2024-03-26
ExomeGermlineSingleSample 3.1.22 2024-06-12
UltimaGenomicsWholeGenomeGermline 1.0.19 2024-06-12
WholeGenomeGermlineSingleSample 3.2.1 2024-06-12
VariantCalling 2.2.1 2024-06-12
UltimaGenomicsJointGenotyping 1.1.7 2023-12-18
JointGenotyping 1.6.10 2023-12-18
JointGenotypingByChromosomePartOne 1.4.12 2023-12-18
ReblockGVCF 2.2.1 2024-06-12
JointGenotypingByChromosomePartTwo 1.4.11 2023-12-18
UltimaGenomicsJointGenotyping 1.1.7 2023-12-18
ReblockGVCF 2.1.12 2024-03-26
ExomeGermlineSingleSample 3.1.19 2024-03-26
UltimaGenomicsWholeGenomeGermline 1.0.16 2024-03-26
WholeGenomeGermlineSingleSample 3.1.20 2024-03-26
RNAWithUMIsPipeline 1.0.16 2023-12-18
CheckFingerprint 1.0.16 2024-03-26
ValidateChip 1.16.4 2023-12-18
Imputation 1.1.12 2023-12-18
JointGenotypingByChromosomePartOne 1.4.12 2023-12-18
ExternalExomeReprocessing 3.2.1 2024-06-12
ExternalWholeGenomeReprocessing 2.2.1 2024-06-12
ExomeReprocessing 3.2.1 2024-06-12
CramToUnmappedBams 1.1.2 2022-04-14
WholeGenomeReprocessing 3.2.1 2024-06-12
IlluminaGenotypingArray 1.12.20 2024-06-12
Arrays 2.6.26 2024-06-12
MultiSampleArrays 1.6.1 2022-04-14
Arrays 2.6.23 2024-03-26
ValidateChip 1.16.4 2023-12-18
Imputation 1.1.13 2024-05-21
RNAWithUMIsPipeline 1.0.16 2023-12-18
BroadInternalUltimaGenomics 1.0.20 2024-06-12
BroadInternalArrays 1.1.10 2024-06-12
BroadInternalImputation 1.1.11 2024-05-21
BroadInternalRNAWithUMIs 1.0.32 2024-06-12
CheckFingerprint 1.0.19 2024-06-12
AnnotationFiltration 1.2.5 2023-12-18
1 change: 1 addition & 0 deletions website/docs/Pipelines/snM3C/README.md
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Expand Up @@ -89,6 +89,7 @@ To see specific tool parameters, select the [workflow WDL link](https://github.c
| Task name | Tool | Software | Description |
| --- | --- | --- | --- |
| Demultiplexing | Cutadapt | [Cutadapt](https://cutadapt.readthedocs.io/en/stable/) | Performs demultiplexing to cell-level FASTQ files based on random primer indices. |
| Summary_PerCellOutput | --- | --- | Untar files needed at per cell level |
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| Hisat-paired-end | Cutadapt, HISAT-3N, [hisat3n_general.py](https://github.com/lhqing/cemba_data/blob/788e83cd66f3b556bdfacf3485bed9500d381f23/cemba_data/hisat3n/hisat3n_general.py), [hisat3n_m3c.py](https://github.com/lhqing/cemba_data/blob/bf6248239074d0423d45a67d83da99250a43e50c/cemba_data/hisat3n/hisat3n_m3c.py) | [Cutadapt](https://cutadapt.readthedocs.io/en/stable/), [HISAT-3N](https://daehwankimlab.github.io/hisat2/hisat-3n/), python3 | Sorts, filters, and trims reads using the `r1_adapter`, `r2_adapter`, `r1_left_cut`, `r1_right_cut`, `r2_left_cut`, and `r2_right_cut` input parameters; performs paired-end read alignment; imports 2 custom python3 scripts developed by Hanqing Liu and calls the `separate_unique_and_multi_align_reads()` and `split_hisat3n_unmapped_reads()` functions to separate unmapped, uniquely aligned, multi-aligned reads from HISAT-3N BAM file, then splits the unmapped reads FASTQ file by all possible enzyme cut sites and output new R1 and R2 FASTQ files; unmapped reads are stored in unmapped FASTQ files and uniquely and multi-aligned reads are stored in separate BAM files. |
| Hisat_single_end | HISAT-3N, [hisat3n_m3c.py](https://github.com/lhqing/cemba_data/blob/bf6248239074d0423d45a67d83da99250a43e50c/cemba_data/hisat3n/hisat3n_m3c.py) | [HISAT-3N](https://daehwankimlab.github.io/hisat2/hisat-3n/), python3 | Performs single-end alignment of unmapped reads to maximize read mapping, imports a custom python3 script developed by Hanqing Liu, and calls the `remove_overlap_read_parts()` function to remove overlapping reads from the split alignment BAM file produced during single-end alignment. |
| Merge_sort_analyze | merge, sort, MarkDuplicates, [hisat3n_m3c.py](https://github.com/lhqing/cemba_data/blob/bf6248239074d0423d45a67d83da99250a43e50c/cemba_data/hisat3n/hisat3n_m3c.py), bam-to-allc, extract-allc | [samtools](https://www.htslib.org/), [Picard](https://broadinstitute.github.io/picard/), python3, [ALLCools](https://lhqing.github.io/ALLCools/intro.html) | Merges and sorts all mapped reads from the paired-end and single-end alignments; creates a position-sorted BAM file and a name-sorted BAM file; removes duplicate reads from the position-sorted, merged BAM file; imports a custom python3 script developed by Hanqing Liu and calls the `call_chromatin_contacts()` function to call chromatin contacts from the name-sorted, merged BAM file; reads are considered chromatin contacts if they are greater than 2,500 base pairs apart; creates a first ALLC file with a list of methylation points and a second ALLC file containing methylation contexts. |
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