43 projects
bam-readgroup-to-json
convert each readgroup id to a json file from a BAM
bam-reheader
reheader a BAM to include GDC @SQ info
gdc-readgroups
From a BAM, convert each readgroup to a json/tsv object needed to create a GDC Read Group node.
picard_metrics_sqlite
store picard metrics in sqlite
json-to-sqlite
convert to json to column based sqlite
fastq_to_SAM_PU
extract a PU value from a fastq record
integrity_to_sqlite
store `ls -l`, `md5sum` and `sha256sum` to sqlite
readgroup_json_db
read readgroup data as json and store in sqlitedb
merge_sqlite
merge arbitrary number of sqlite files
fastqc_db
store FastQC data/summary in sqlitedb
samtools_metrics_sqlite
store samtools metrics in sqlite
sqlite_to_postgres
write sqlite file to postgres
bunny_runtime_metrics_sqlite
store bunny runtime metrics in sqlite
star_metrics_sqlite
store star metrics in sqlite
fastqvalidator_sqlite
store fastqvalidator metrics in sqlite
dnaseq_queue_status
write db status
dnaseq_validation
validate dnaseq workflow based on fastqc, picard and samtools metrics
queue_bqsr_status
write bqsr db status
table_string_sqlite_cell
create a single cell table with a value
optityper_to_sqlite
store optityper metrics in sqlite
queue_hlatype_status
write hlatyping db status
queue_coclean_status
write coclean db status
fastqc_to_json
fastqc to json for bwa cwl
queue_status
write db status
cgquery_xml_to_bamlibrary_capture_json
convert cgquery sra xml to capture_kits/target_set json
fastq_remove_duplicate_qname
remove duplicate QNAME from a fastq
picard_tool
call picard tools and store time/mem metrics in sqlitedb
bwa_pe_tool
map PE fastq reads to a reference genome with bwa
decider_bwa_pe
match readgroup and fastq outputs
decider_bwa_se
match readgroup and fastq outputs
bwa_tool
map PE fastq reads to a reference genome with bwa
bwa_se_tool
map SE fastq reads to a reference genome with bwa
bam_add_eof
if a BAM is missing EOF, add it, else output original BAM
remove_duplicate_fastq_matepair
Remove duplicate mate pairs from a FASTQ
fastqc_tool
call fastqc tools and store time/mem metrics in sqlitedb
biobambam_tool
call biobambam tools and store time/mem metrics in sqlitedb
samtools_tool
call samtools tools and store time/mem metrics in sqlitedb
cdis_pipe_utils
Reusable code to call pipeline tools and get time/mem metrics
fastqc_sqlite
store FastQC data/summary in sqlitedb
readgroup_platform_insertion
Insert a PL:<value> in @RGs in a BAM header
sra_hs_lookup
call remove_qcfailed_mapped and store time/mem metrics in sqlitedb
remove_qcfailed_mapped
call remove_qcfailed_mapped and store time/mem metrics in sqlitedb
bamutil_tool
call bamutil tools and store time/mem metrics in sqlitedb
