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Username    jeremiahsavage
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43 projects

bam-readgroup-to-json

Last released

convert each readgroup id to a json file from a BAM

bam-reheader

Last released

reheader a BAM to include GDC @SQ info

gdc-readgroups

Last released

From a BAM, convert each readgroup to a json/tsv object needed to create a GDC Read Group node.

picard_metrics_sqlite

Last released

store picard metrics in sqlite

json-to-sqlite

Last released

convert to json to column based sqlite

fastq_to_SAM_PU

Last released

extract a PU value from a fastq record

integrity_to_sqlite

Last released

store `ls -l`, `md5sum` and `sha256sum` to sqlite

readgroup_json_db

Last released

read readgroup data as json and store in sqlitedb

merge_sqlite

Last released

merge arbitrary number of sqlite files

fastqc_db

Last released

store FastQC data/summary in sqlitedb

samtools_metrics_sqlite

Last released

store samtools metrics in sqlite

sqlite_to_postgres

Last released

write sqlite file to postgres

bunny_runtime_metrics_sqlite

Last released

store bunny runtime metrics in sqlite

star_metrics_sqlite

Last released

store star metrics in sqlite

fastqvalidator_sqlite

Last released

store fastqvalidator metrics in sqlite

dnaseq_queue_status

Last released

write db status

dnaseq_validation

Last released

validate dnaseq workflow based on fastqc, picard and samtools metrics

queue_bqsr_status

Last released

write bqsr db status

table_string_sqlite_cell

Last released

create a single cell table with a value

optityper_to_sqlite

Last released

store optityper metrics in sqlite

queue_hlatype_status

Last released

write hlatyping db status

queue_coclean_status

Last released

write coclean db status

fastqc_to_json

Last released

fastqc to json for bwa cwl

queue_status

Last released

write db status

cgquery_xml_to_bamlibrary_capture_json

Last released

convert cgquery sra xml to capture_kits/target_set json

fastq_remove_duplicate_qname

Last released

remove duplicate QNAME from a fastq

picard_tool

Last released

call picard tools and store time/mem metrics in sqlitedb

bwa_pe_tool

Last released

map PE fastq reads to a reference genome with bwa

decider_bwa_pe

Last released

match readgroup and fastq outputs

decider_bwa_se

Last released

match readgroup and fastq outputs

bwa_tool

Last released

map PE fastq reads to a reference genome with bwa

bwa_se_tool

Last released

map SE fastq reads to a reference genome with bwa

bam_add_eof

Last released

if a BAM is missing EOF, add it, else output original BAM

remove_duplicate_fastq_matepair

Last released

Remove duplicate mate pairs from a FASTQ

fastqc_tool

Last released

call fastqc tools and store time/mem metrics in sqlitedb

biobambam_tool

Last released

call biobambam tools and store time/mem metrics in sqlitedb

samtools_tool

Last released

call samtools tools and store time/mem metrics in sqlitedb

cdis_pipe_utils

Last released

Reusable code to call pipeline tools and get time/mem metrics

fastqc_sqlite

Last released

store FastQC data/summary in sqlitedb

readgroup_platform_insertion

Last released

Insert a PL:<value> in @RGs in a BAM header

sra_hs_lookup

Last released

call remove_qcfailed_mapped and store time/mem metrics in sqlitedb

remove_qcfailed_mapped

Last released

call remove_qcfailed_mapped and store time/mem metrics in sqlitedb

bamutil_tool

Last released

call bamutil tools and store time/mem metrics in sqlitedb

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