MANIFEST

.dockerignore
bin/viv.pl
bin/vtfp.pl
Build.PL
Changes
data/bcl2bam_phix_deplex_wtsi_stage1_template.vtf
data/bwa_post_proc.vtf
data/hiseqx.vtf
data/post_alignment.vtf
data/static_params/stage2_reanalysis/align_bwa_mem2.json
data/static_params/stage2_reanalysis/base_params_duplexseq_cram.json
data/static_params/stage2_reanalysis/base_params_duplexseq_fastq.json
data/static_params/stage2_reanalysis/base_params_samtools_cram.json
data/static_params/stage2_reanalysis/base_params_samtools_nchs.json
data/static_params/stage2_reanalysis/base_params_samtools_nchs_fastq.json
data/static_params/stage2_reanalysis/base_params_samtools_ysplit_nta_cram.json
data/static_params/stage2_reanalysis/nchs_ref_defaults.json
data/vtlib/alignment_common.json
data/vtlib/alignment_wtsi_stage2_humansplit_extrasplit_notargetalign_template.json
data/vtlib/alignment_wtsi_stage2_humansplit_notargetalign_template.json
data/vtlib/alignment_wtsi_stage2_humansplit_template.json
data/vtlib/alignment_wtsi_stage2_template.json
data/vtlib/auxmerge_prep.json
data/vtlib/auxmerge_prep_realign.json
data/vtlib/bamindexdecoder.json
data/vtlib/basic_params_top_up_merge.json
data/vtlib/bcftools_genotype_call.json
data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json
data/vtlib/bwa_aln_alignment.json
data/vtlib/bwa_aln_se_alignment.json
data/vtlib/bwa_mem_alignment.json
data/vtlib/bwa_mem_bwakit_alignment.json
data/vtlib/c2a.json
data/vtlib/crammerge.json
data/vtlib/final_output_noalign_prep.json
data/vtlib/final_output_prep.json
data/vtlib/final_output_prep_chrsplit_noaln.json
data/vtlib/final_stage1_process.json
data/vtlib/final_stage1_process_nosplit.json
data/vtlib/haplotagging.json
data/vtlib/hisat2_alignment.json
data/vtlib/markdup_biobambam.json
data/vtlib/markdup_duplexseq.json
data/vtlib/markdup_none.json
data/vtlib/markdup_picard.json
data/vtlib/markdup_samtools.json
data/vtlib/merge_aligned.json
data/vtlib/merge_final_output_prep.json
data/vtlib/merged_markdup_biobambam.json
data/vtlib/merged_markdup_samtools.json
data/vtlib/minimap2_alignment.json
data/vtlib/passthrough.json
data/vtlib/post_alignment.json
data/vtlib/post_alignment_realignment.json
data/vtlib/pre_alignment.json
data/vtlib/pre_alignment_realign.json
data/vtlib/read2tags.json
data/vtlib/README.vtlib
data/vtlib/realignment_wtsi_humansplit_notargetalign_template.json
data/vtlib/realignment_wtsi_humansplit_template.json
data/vtlib/realignment_wtsi_template.json
data/vtlib/salmon_alignment.json
data/vtlib/seqchksum.json
data/vtlib/seqchksum_ehs.json
data/vtlib/seqchksum_hs.json
data/vtlib/seqchksum_realign.json
data/vtlib/seqchksum_stage1.json
data/vtlib/split_by_chromosome.json
data/vtlib/stage2_preprocess_inputs.json
data/vtlib/star_alignment.json
data/vtlib/subsample.json
data/vtlib/subsample_spec_frac.json
data/vtlib/subsample_tmf.json
data/vtlib/target_alignment.json
data/vtlib/target_nchs_alignment.json
data/vtlib/tophat2_alignment.json
data/vtlib/unaln_intfile.json
data/vtlib/unaln_intfile4.json
data/vtlib/unaln_tee3.json
data/vtlib/unaln_tee4.json
Dockerfile
examples/bwa_aln_cfg.png
examples/bwa_mem/bwa_mem_alignment.vtf
examples/bwa_mem/generic_alignment_with_phix.vtf
examples/bwa_mem/post_alignment.vtf
examples/bwa_mem/post_alignment_filter.vtf
examples/bwa_mem/README.bwa_mem
examples/bwa_mem/seqchksum.vtf
examples/example_01.cfg
examples/example_02.cfg
examples/example_03.cfg
examples/example_04.cfg
examples/README.examples.md
examples/tophat2_cfg.png
MANIFEST			This list of files
README
README.md
README.vtfp
scripts/install_npg_perl_dependencies.sh
supplement/dehumanise/scripts/dh_publish.sh
supplement/dehumanise/scripts/dh_refresh_manifest.sh
supplement/dehumanise/scripts/dh_submit.sh
supplement/dehumanise/scripts/ftc_env.sh
supplement/dehumanise/templates/dehumaniser.json
supplement/dehumanise/templates/filter_chain.json
supplement/dehumanise/templates/filter_human.json
supplement/dehumanise/templates/filter_human_dehumaniser.json
supplement/dehumanise/templates/filter_twochain.json
supplement/dehumanise/templates/ftc_base_pv_in.json
supplement/dehumanise/templates/kraken2_human_qn.json
supplement/dehumanise/templates/passthrough.json
supplement/dehumanise/templates/sq_fix.json
supplement/dehumanise/utils/covid_hdr_fix.pl
supplement/dehumanise/utils/filter_by_qn.pl
supplement/dehumanise/utils/filter_by_taxid9606.pl
t/00-scripts_compile.t
t/10-viv-noop_edge.t
t/10-viv-packflag.t
t/10-viv-stringify.t
t/10-viv-teenode.t
t/10-vtfp-array_expansion.t
t/10-vtfp-noop.t
t/10-vtfp-param_ring.t
t/10-vtfp-pv.t
t/10-vtfp-select_directive.t
t/10-vtfp-select_directive.v2.t
t/10-vtfp-splice_nodes.t
t/10-vtfp-subst_directive.t
t/10-vtfp-subst_directive.v2.t
t/10-vtfp-vtfile.t
t/10-vtfp-vtfile_v2.t
t/50-viv.t
t/data/10-vtfp-array_expansion.json
t/data/10-vtfp-array_expansion.v2.json
t/data/10-vtfp-noop.json
t/data/10-vtfp-param_ring.json
t/data/10-vtfp-pv.json
t/data/10-vtfp-splice_nodes_00.json
t/data/50-viv_failing_io_pipeline0.v2.vtf
t/data/50-viv_failing_io_pipeline0.vtf
t/data/50-viv_failing_io_pipeline1.v2.vtf
t/data/50-viv_failing_io_pipeline1.vtf
t/data/50-viv_failing_io_pipeline2.v2.vtf
t/data/50-viv_failing_io_pipeline2.vtf
t/data/50-viv_failing_pipeline.v2.vtf
t/data/50-viv_failing_pipeline.vtf
t/data/50-viv_pipeline.v2.vtf
t/data/50-viv_pipeline.vtf
visualisation/bwa_aln.cfg
visualisation/bwa_aln.json
visualisation/cgi-bin/getProgress
visualisation/config_view.html
visualisation/edit.html
visualisation/p4_edit.css
visualisation/p4_edit.js
visualisation/README.visualisation
visualisation/tophat2.cfg
visualisation/tophat2.json
visualisation/view.js