ENCODE-DCC rna-seq-pipeline issues

ENCODE-DCC / rna-seq-pipeline

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There's two files of "transcript quantifications" without any reasonable way to tell them apart in the metadata file ?

#103 PanosFirmpas opened 9 months ago
0
workflow help

#102 songxh1996 opened 1 year ago
0
question on strandedness option

#101 adalgarno opened 1 year ago
2
CVE-2007-4559 Patch

#100 TrellixVulnTeam opened 1 year ago
0
Error when testing build_genome_index.wdl: GRCh38_no_alt_analysis_set_GCA_000001405.15_onlychr19.fa.gz: No such file or directory

#99 liboxun closed 2 years ago
2
sample_genome.bam and sample_anno.bam cannot be opened by pipeline

#98 liboxun closed 2 years ago
2
Update align.py

#97 byee4 closed 2 years ago
0
error when using croo to generate report

#96 yr-gh opened 2 years ago
4
SAM header has duplicate sorting order (SO) fields

#95 zaeleus opened 2 years ago
0
Pipe 60 update howto doc and fix singularity

#94 leepc12 closed 2 years ago
0
call-kallisto/shard-1/attempt-2/execution/script: line 23: python3: command not found

#93 byee4 closed 2 years ago
11
PIPE-42-base-image

#92 ottojolanki closed 2 years ago
0
Pipeline hanging during rna.align; waiting for return code

#91 ghost closed 1 year ago
9
PIP-1638-docker-image-workflow-input

#90 ottojolanki closed 2 years ago
1
shell /bin/sh does not exist in container when running with singularity

#89 westonkjones opened 2 years ago
3
unknown option --fastqs_R1

#88 jaavedm closed 2 years ago
2
PIP-1618-dockstore

#87 ottojolanki closed 2 years ago
0
Running with Conda Environment?

#86 CharaiCC closed 3 years ago
1
Schematic Describing Pipeline?

#85 YogiOnBioinformatics closed 3 years ago
2
PIP-1583-pbam

#84 ottojolanki closed 3 years ago
0
Added documentation for running on Truwl.

#83 ksebby closed 3 years ago
0
Issue running the test case

#82 lwtan90 closed 3 years ago
0
Can't find log.final.out

#81 ishujain4695 closed 3 years ago
3
Errors with dependent software

#80 rameshvnair closed 3 years ago
2
ConnectionResetError

#79 User-yx closed 3 years ago
1
WDL meta, versioning, tests in caper

#78 ottojolanki closed 3 years ago
0
PIP-1312-test-with-caper

#77 ottojolanki closed 3 years ago
0
PIP-1472-quickcheck-bams (#75)

#76 ottojolanki closed 3 years ago
0
PIP-1472-quickcheck-bams

#75 ottojolanki closed 3 years ago
1
rna.align error when attempting to run pipeline on test data

#74 gilesc closed 3 years ago
4
PIP-1407-update-images

#73 ottojolanki closed 3 years ago
0
kallisto fragment length input to Array in example

#72 ottojolanki closed 3 years ago
0
Running in Google Cloud fails with: Scopes not configured for service account

#71 TomGardner closed 3 years ago
4
hotfix: change color to fix graphviz warning

#70 leepc12 closed 3 years ago
0
hotfix: add task graph to croo def JSON

#69 leepc12 closed 3 years ago
0
bedGraphToBigWig: needLargeMem: trying to allocate 0 bytes (limit: 100000000000)

#68 User-yx closed 4 years ago
2
caper

#67 User-yx closed 4 years ago
2
"rna.run_kallisto": "false"

#66 User-yx closed 4 years ago
11
PIP-1310-dockerhub

#65 ottojolanki closed 4 years ago
0
v1.2.0

#64 ottojolanki closed 4 years ago
0
PIP-1274-multiple-fragment-sizes

#63 ottojolanki closed 4 years ago
0
PIP-1226-test-files-to-bucket

#62 ottojolanki closed 4 years ago
0
PIP-1195-version-to-metadata

#61 ottojolanki closed 4 years ago
0
PIP-1172-wdl-1.0

#60 ottojolanki closed 4 years ago
0
format spaces

#59 ottojolanki closed 4 years ago
0
PIP-1181-format

#58 ottojolanki closed 4 years ago
0
HTML QC Report

#57 YogiOnBioinformatics closed 4 years ago
2
PIP-1110-kallisto-optional

#56 ottojolanki closed 4 years ago
0
Starting with BAMs

#55 YogiOnBioinformatics closed 4 years ago
2
PIP-979-rna-aligner-purge

#54 ottojolanki closed 4 years ago
1