<commit_before>## STLI: Disclaimer: the versions in tool paths described here should be the actual versions used at all times
BWA_PATH	/data/tools/bwa_v0.7.5a
SAMBAMBA_PATH	/data/tools/sambamba_v0.6.5
SAMTOOLS_PATH	/data/tools/samtools_v1.2

BAMMETRICS_PATH	/data/tools/bammetrics_v2.1.4
PICARD_PATH	/data/tools/picard-tools_v1.141
DAMAGE_ESTIMATOR_PATH	/data/tools/damage_estimator_v1.0
BAMUTIL_PATH	/data/tools/bamutil_v1.0.13/bin

GATK_PATH	/data/tools/gatk_v3.8.0
GATK_QUEUE_PATH	/data/tools/gatk_v3.8.0

STRELKA_PATH	/data/tools/strelka_v1.0.14
STRELKA_POST_PROCESS_PATH	/data/tools/strelka-post-process_v1.4

AMBER_PATH	/data/tools/amber_v1.6
COBALT_PATH	/data/tools/cobalt_v1.4
PURPLE_PATH	/data/tools/purple_v2.14
CIRCOS_PATH	/data/tools/circos_v0.69.6/bin

MANTA_PATH	/data/tools/manta_v1.0.3/bin
BPI_PATH	/data/tools/break-point-inspector_v1.7
GRIDSS_PATH	/data/tools/gridss_v2.0.1
GRIDSS_BWA_PATH	/data/tools/bwa_v0.7.17

SNPEFF_PATH	/data/tools/snpEff_v4.3s
BCFTOOLS_PATH	/data/tools/bcftools_v1.3.1
TABIX_PATH	/data/tools/tabix_v0.2.6

HEALTH_CHECKER_PATH	/data/tools/healthchecker_v2.4

REALIGNMENT_SCALA	IndelRealignment.scala
BASERECALIBRATION_SCALA	BaseRecalibration.scala
GERMLINE_CALLING_SCALA	GermlineCaller.scala
GERMLINE_FILTER_SCALA	GermlineFilter.scala

REPORT_STATUS	/usr/bin/env true<commit_msg>DEV-618: Bump purple to v2.17<commit_after>## STLI: Disclaimer: the versions in tool paths described here should be the actual versions used at all times
BWA_PATH	/data/tools/bwa_v0.7.5a
SAMBAMBA_PATH	/data/tools/sambamba_v0.6.5
SAMTOOLS_PATH	/data/tools/samtools_v1.2

BAMMETRICS_PATH	/data/tools/bammetrics_v2.1.4
PICARD_PATH	/data/tools/picard-tools_v1.141
DAMAGE_ESTIMATOR_PATH	/data/tools/damage_estimator_v1.0
BAMUTIL_PATH	/data/tools/bamutil_v1.0.13/bin

GATK_PATH	/data/tools/gatk_v3.8.0
GATK_QUEUE_PATH	/data/tools/gatk_v3.8.0

STRELKA_PATH	/data/tools/strelka_v1.0.14
STRELKA_POST_PROCESS_PATH	/data/tools/strelka-post-process_v1.4

AMBER_PATH	/data/tools/amber_v1.6
COBALT_PATH	/data/tools/cobalt_v1.4
PURPLE_PATH	/data/tools/purple_v2.17
CIRCOS_PATH	/data/tools/circos_v0.69.6/bin

MANTA_PATH	/data/tools/manta_v1.0.3/bin
BPI_PATH	/data/tools/break-point-inspector_v1.7
GRIDSS_PATH	/data/tools/gridss_v2.0.1
GRIDSS_BWA_PATH	/data/tools/bwa_v0.7.17

SNPEFF_PATH	/data/tools/snpEff_v4.3s
BCFTOOLS_PATH	/data/tools/bcftools_v1.3.1
TABIX_PATH	/data/tools/tabix_v0.2.6

HEALTH_CHECKER_PATH	/data/tools/healthchecker_v2.4

REALIGNMENT_SCALA	IndelRealignment.scala
BASERECALIBRATION_SCALA	BaseRecalibration.scala
GERMLINE_CALLING_SCALA	GermlineCaller.scala
GERMLINE_FILTER_SCALA	GermlineFilter.scala

REPORT_STATUS	/usr/bin/env true
{'fraction_non_alphanumeric': 0.09668924003009782, 'fraction_numerical': 0.05191873589164785, 'mean_word_length': 5.4072289156626505, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '328755', 'n_tokens_mistral': 1335, 'n_tokens_neox': 1285, 'n_words': 155}