Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Updating pairtools from 1.0.3 to 1.1.0 #5974

Merged
merged 6 commits into from
Apr 30, 2024
Merged
Changes from 4 commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion tools/pairtools/dedup.xml
Original file line number Diff line number Diff line change
@@ -20,7 +20,7 @@
]]></command>
<inputs>
<param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam" label="Input pairs file" help="Input triu-flipped sorted .pairs or .pairsam file"/>
<param argument="--mark-dups" type="boolean" truevalue="--mark-dups" falsevalue="" checked="False" label="Duplicate pairs are marked as DD in pair_type and as a duplicate in the SAM entries"/>
<param argument="--mark-dups" type="boolean" truevalue="--mark-dups" falsevalue="" checked="True" label="Duplicate pairs are marked as DD in pair_type and as a duplicate in the SAM entries"/>
<param argument="--output-dups" type="boolean" truevalue="--output-dups" falsevalue="" checked="False" label="Output file for duplicate pairs"/>
<param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Output file for duplicate statistics"/>
</inputs>
4 changes: 2 additions & 2 deletions tools/pairtools/macros.xml
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
<macros>
<token name="@TOOL_VERSION@">1.0.3</token>
<token name="@SUFFIX_VERSION@">0</token>
<token name="@TOOL_VERSION@">1.1.0</token>
<token name="@SUFFIX_VERSION@">1</token>
SaimMomin12 marked this conversation as resolved.
Show resolved Hide resolved
<xml name="edam_ontology">
<edam_datas>
<edam_data>topic_1381</edam_data>
2 changes: 1 addition & 1 deletion tools/pairtools/parse.xml
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy1" profile="23.2" license="MIT">
<tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy0" profile="23.2" license="MIT">
SaimMomin12 marked this conversation as resolved.
Show resolved Hide resolved
<description>Find ligation pairs in alignments and create pairs.</description>
<macros>
<import>macros.xml</import>
8 changes: 4 additions & 4 deletions tools/pairtools/test-data/output_dedup_pairs.pairsam
Original file line number Diff line number Diff line change
@@ -39,20 +39,20 @@
#samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz
#samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa VN:1.0.2
#samheader: @PG ID:pairtools_sort-1.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-1.2 VN:1.0.2
#samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs.pairsam output_sorted_pairs.pairsam PP:pairtools_sort-1.3 VN:1.0.2
#samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/2/1/3/dataset_21372a8a-66a4-4ab8-8a38-a1e4d87d5048.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/2/outputs/dataset_b7034ba7-f57e-4752-a341-425fdb4da81e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-1.3 VN:1.1.0
#samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz
#samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-2CCE5976 VN:1.0.2
#samheader: @PG ID:pairtools_sort-2.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-2.2 VN:1.0.2
#samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs.pairsam output_sorted_pairs.pairsam PP:pairtools_sort-2.3 VN:1.0.2
#samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/2/1/3/dataset_21372a8a-66a4-4ab8-8a38-a1e4d87d5048.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/2/outputs/dataset_b7034ba7-f57e-4752-a341-425fdb4da81e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-2.3 VN:1.1.0
#samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz
#samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-3CAFD9D9 VN:1.0.2
#samheader: @PG ID:pairtools_sort-3.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-3.2 VN:1.0.2
#samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs.pairsam output_sorted_pairs.pairsam PP:pairtools_sort-3.3 VN:1.0.2
#samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/2/1/3/dataset_21372a8a-66a4-4ab8-8a38-a1e4d87d5048.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/2/outputs/dataset_b7034ba7-f57e-4752-a341-425fdb4da81e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-3.3 VN:1.1.0
#samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz
#samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam
#samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:samtools VN:1.0.2
#samheader: @PG ID:pairtools_sort-4.4 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-4.3 VN:1.0.2
#samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs.pairsam output_sorted_pairs.pairsam PP:pairtools_sort-4.4 VN:1.0.2
#samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/2/1/3/dataset_21372a8a-66a4-4ab8-8a38-a1e4d87d5048.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/2/outputs/dataset_b7034ba7-f57e-4752-a341-425fdb4da81e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-4.4 VN:1.1.0
#columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2
HWI-ST560:29:B0A7LABXX:2:1101:15566:24141 chrI 3199 chrI 3399 + - UU HWI-ST560:29:B0A7LABXX:2:1101:15566:2414197chrI31996015S35M=3350201CTTAGACAATAAGCTAGCTTTCAAGATATAAGATACGAAATAGGGGTTGA111442422223232232<FHIIIIBCCFHEHFHHIHCGIJIDHHJ?@FHNM:i:0MD:Z:35AS:i:35XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:15566:24141145chrI33506050M=3199-201TAGAATCTCCCATGTCAACGGGTTTCCATACCTCCCCAGCATCATACATCGHHGFAGFJJJIHHFGD?HIGCGHGHHHFAFC<IHFACHDAFDEDADB==NM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU
HWI-ST560:29:B0A7LABXX:2:1101:18861:21891 chrI 35431 chrI 35703 + - UU HWI-ST560:29:B0A7LABXX:2:1101:18861:2189197chrI354316050M=35654273GACCACGTGGTCGTTGATGCTGCCAGCAGTTGTGCAGACCTGCATTGCTG114442222322<2@FEAFHFH<CFHFFH?GH:CDHGGIGEFDG<BBH9?NM:i:1MD:Z:35G14AS:i:45XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:18861:21891145chrI356546050M=35431-273ATGTGGCTGCTTTAATTGAGCCTCTTTCTGTCACCTGGCATGCTGTTAAG>EGDD?BFIIIIGBHCJIJIHFIHFHGHGGC<2GHGHFD<HFFDDDDB@BNM:i:1MD:Z:14G35AS:i:45XS:i:0Yt:Z:UU
Loading