Finish/Verify conversions from CWL

[chrisamiller]

The following text is taken from the old README at the root of this repository. I am unsure how many of these have yet to be converted, but it's worth looking through, verifying missing pieces, and making a decision to convert or omit.

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Conversions

Pipelines

• alignment_exome
• alignment_exome_nonhuman
• alignment_umi_duplex
  # this depends on a thing with non-trivial embedded javascript
• alignment_umi_molecular
  # this depends on a thing with non-trivial embedded javascript
• alignment_wgs
• alignment_wgs_nonhuman
• aml_trio_cle
• aml_trio_cle_gathered # This doesn't make sense in cloud
• bisulfite
• chipseq
  # This depends on homer-tag-directory, doesn't make sense in cloud
• chipseq_alignment_nonhuman
  # This depends on homer-tag-directory, doesn't make sense in cloud
• detect_variants
• detect_variants_nonhuman
• detect_variants_wgs
• downsample_and_recall
• gathered_downsample_and_recall # This doesn't make sense in cloud
• germline_exome
• germline_exome_gvcf
• germline_exome_hla_typing
• germline_wgs
• germline_wgs_gvcf
• immuno
• rnaseq
• rnaseq_star_fusion
• rnaseq_star_fusion_with_xenosplit
• somatic_exome
• somatic_exome_cle
• somatic_exome_cle_gathered # This doesn't make sense in cloud
• somatic_exome_gathered # This doesn't make sense in cloud
• somatic_exome_nonhuman
• somatic_wgs
• tumor_only_detect_variants
• tumor_only_exome
• tumor_only_wgs

Subworkflows

• align
• align_sort_markdup
• bam_readcount
• bam_to_trimmed_fastq_and_hisat_alignments
• bgzip_and_index
• bisulfite_qc
• cellranger_mkfastq_and_count
• cnvkit_single_sample
• cram_to_bam_and_index
• cram_to_cnvkit
• docm_cle
• docm_germline
• duplex_alignment
• filter_vcf
• filter_vcf_nonhuman
• fp_filter
• gatk_haplotypecaller_iterator
• germline_detect_variants
• germline_filter_vcf
• hs_metrics
• joint_genotype
• merge_svs
• molecular_alignment
• molecular_qc
• mutect
• phase_vcf
• pindel
• pindel_cat
• pindel_region
• pvacseq
• qc_exome
• qc_exome_no_verify_bam
• qc_wgs
• qc_wgs_nonhuman
• sequence_align_and_tag_adapter
• sequence_to_bqsr
• sequence_to_bqsr_nonhuman
• sequence_to_trimmed_fastq
• sequence_to_trimmed_fastq_and_biscuit_alignments
• single_cell_rnaseq
• single_sample_sv_callers
• strelka_and_post_processing
• strelka_process_vcf
• sv_depth_caller_filter
• sv_paired_read_caller_filter
• umi_alignment
• varscan
• varscan_germline
• varscan_pre_and_post_processing
• vcf_eval_cle_gold
• vcf_eval_concordance
• vcf_readcount_annotator

Tools

• add_strelka_gt
• add_string_at_line
• add_string_at_line_bgzipped
• add_vep_fields_to_table
• agfusion
• align_and_tag
• annotsv
• annotsv_filter
• apply_bqsr
• bam_readcount
• bam_to_bigwig
• bam_to_cram
• bam_to_fastq
• bam_to_sam
• bcftools_merge
• bedgraph_to_bigwig
• bedtools_intersect
• bgzip
• biscuit_align
• biscuit_markdup
• biscuit_pileup
• bisulfite_qc_conversion
• bisulfite_qc_coverage_stats
• bisulfite_qc_cpg_retention_distribution
• bisulfite_qc_mapping_summary
• bisulfite_vcf2bed
• bqsr
• call_duplex_consensus
• call_molecular_consensus
• cat_all
• cat_out
• cellmatch_lineage
• cellranger_atac_count
• cellranger_count
• cellranger_feature_barcoding
• cellranger_mkfastq
• cellranger_vdj
• cle_aml_trio_report_alignment_stat
• cle_aml_trio_report_coverage_stat
• cle_aml_trio_report_full_variants
• clip_overlap
• cnvkit_batch
• cnvkit_vcf_export
• cnvnator
• collect_alignment_summary_metrics
• collect_gc_bias_metrics
• collect_hs_metrics
• collect_insert_size_metrics
• collect_wgs_metrics
• combine_gvcfs
• combine_variants
• combine_variants_concordance
• combine_variants_wgs
• concordance
• cram_to_bam
• docm_add_variants
• docm_gatk_haplotype_caller
• downsample
• duphold
• duplex_seq_metrics
• eval_cle_gold
• eval_vaf_report
• extract_hla_alleles
• extract_umis
• fastq_to_bam
• filter_consensus
• filter_known_variants
• filter_sv_vcf_blocklist_bedpe
• filter_sv_vcf_depth
• filter_sv_vcf_read_support
• filter_sv_vcf_size
• filter_vcf_cle
• filter_vcf_coding_variant
• filter_vcf_custom_allele_freq
• filter_vcf_depth
• filter_vcf_docm
• filter_vcf_mapq0
• filter_vcf_somatic_llr
• fix_vcf_header
• fp_filter
• gather_to_sub_directory
• gatherer
• gatk_genotypegvcfs
• gatk_haplotype_caller
• generate_qc_metrics
• germline_combine_variants
• grolar
• group_reads
• hisat2_align
• hla_consensus
• homer_tag_directory
  # This doesn't make sense in cloud
• index_bam
• index_cram
• index_vcf
• intersect_known_variants
• interval_list_expand
• intervals_to_bed
• kallisto
• kmer_size_from_index
• manta_somatic
• mark_duplicates_and_sort
• mark_illumina_adapters
• merge_bams
• merge_bams_samtools
• merge_vcf
• mutect
• name_sort
• normalize_variants
• optitype_dna
• picard_merge_vcfs
• pindel
• pindel2vcf
• pindel_somatic_filter
• pizzly
• pvacbind
• pvacfuse
• pvacseq
• pvacseq_combine_variants
• pvacvector
• read_backed_phasing
• realign
• remove_end_tags
• rename
• replace_vcf_sample_name
• samtools_flagstat
• samtools_sort
• select_variants
• sequence_align_and_tag
• sequence_to_bam
  # this uses non-trivial embedded javascript
• sequence_to_fastq
• set_filter_status
• single_sample_docm_filter
• smoove
• somatic_concordance_graph
• sompy
• sort_vcf
• split_interval_list
• split_interval_list_to_bed
• staged_rename
• star_align_fusion
• star_fusion_detect
• strandedness_check
• strelka
• stringtie
• survivor
• transcript_to_gene
• trim_fastq
• umi_align
• variants_to_table
• varscan_germline
• varscan_process_somatic
• varscan_somatic
• vcf_expression_annotator
• vcf_readcount_annotator
• vcf_sanitize
• vep
• verify_bam_id
• vt_decompose
• xenosplit