diff --git a/docs/STAR_2.7.11b_DIPLOID.md b/docs/STAR_2.7.11b_DIPLOID.md
index ca7798a..912fddc 100644
--- a/docs/STAR_2.7.11b_DIPLOID.md
+++ b/docs/STAR_2.7.11b_DIPLOID.md
@@ -90,7 +90,7 @@ These variants get removed during bcftools step of filtering on `PASS`
 These have even more `FILTER` added that are dropped on `PASS`:
  - Common
    - ExcessHet: `ExcessHet > 54.69`
-   - QD2: `QD < 2.0"`
+   - QD2: `QD < 2.0`
    - QUAL30: `QUAL < 30.0`
  - SNP only:
    - SOR3_SNP: `SOR > 3.0`
diff --git a/workflow/kfdrc_star_diploid_wf.cwl b/workflow/kfdrc_star_diploid_wf.cwl
index 4d4231a..27a4142 100644
--- a/workflow/kfdrc_star_diploid_wf.cwl
+++ b/workflow/kfdrc_star_diploid_wf.cwl
@@ -2,7 +2,127 @@ cwlVersion: v1.2
 class: Workflow
 id: kfdrc-star-diploid-wf
 label: KFDRC STAR Diploid Workflow
-doc: "Alignment and quantification by creating a personal genome"
+doc: |-
+  # Kids First Kids First STAR Diploid Beta
+
+  This is an alternative alignment and quantification method currently in **_beta phase_**.
+  It uses a patient's DNA variant calls to create a "personal genome" (PG) for improved alignment.
+  It is purported to have fewer multi-mapping/better unique mapping for potentially improved gene and isoform level quantification.
+  It cannot be used in fusion calling
+  The STAR Diploid mode has a known bug with an unknown cause manifests as a seg fault for up to 20% of normal sample inputs and 100% of tumor inputs. 
+
+  ![data service logo](https://github.com/d3b-center/d3b-research-workflows/raw/master/doc/kfdrc-logo-sm.png)
+
+  ## Introduction
+  This pipeline runs the following steps:
+  1. STAR Genome Generate per individual, or will skip if one has been generated already.
+      -  Strip existing annotations as defined by the user. Since STAR requires an uncompressed vcf, this helps make the input file size smaller as only variant calls and `FORMAT` info are needed
+      -  Filtering steps for input patient DNA variant calls in order to focus on higher quality calls.
+      Recommended filtering criteria recommendations are still being established, but various scenarios and suggestions from our and partner institutions can be found in the inputs section.
+      - Use a genome fasta and gtf - recommend fasta matches input DNA calls - in conjunction with filtered DNA VCF to create PG
+  1. If needed, convert input bam reads to fastq
+  1. If needed, cutadapt to remove any adapters
+  1. Run STAR aligner 
+      - Use PG as refs
+      - Align input reads
+  1. Run custom tool to filter bam for RSEM. Removes indels and soft-clipped reads
+  1. RSEM quantification
+
+  ### Cutadapt
+  [Cutadapt v3.4](https://github.com/marcelm/cutadapt) Cut adapter sequences from raw reads if needed.
+  ### STAR v2.7.11b_alpha_2024-03-29
+  [STAR v2.7.11b_alpha_2024-03-29](https://doi.org/f4h523) RNA-Seq raw data alignment.
+  ### [RSEM](docs/RSEM_1.3.1.md)
+
+  ## INPUTS
+  A brief note - many references and filtering requirements take a bit of up front work. In the [Filtering and Input Appendix](#filtering-and-input-appendix) section, we try to lay this out. The workflow has more inputs that this README will not cover, but can be tweaked by an advanced user.
+  ### Common Required
+  These are inputs used in multiple steps
+   - `output_basename`: String to prepend to results files from STAR and RSEM
+  ### STAR Genome Generate
+  If a pre-existing PG does not exist, need the following inputs to create:
+   - `input_vcf`: Currently not standardized, matched DNA variant calls. For INCLUDE dataset, trio calls were used when available, otherwise singe sample genotyping - both from GATK workflows
+   - `strip_info`: Given that input vcf needs to be uncompressed, stripping `INFO` is a good way to reduce file size. Current recommended strip based on typical KF runs: `INFO/CLNDISDB,INFO/CLNDISDBINCL,INFO/CLNDN,INFO/CLNDNINCL,INFO/CLNHGVS,INFO/CLNREVSTAT,INFO/CLNSIG,INFO/CLNSIGCONF,INFO/CLNSIGINCL,INFO/CLNVC,INFO/CLNVCSO,INFO/CLNVI,INFO/CSQ,INFO/ClippingRankSum,INFO/DB,INFO/DP,INFO/DS,INFO/END,INFO/ExcessHet,INFO/FS,INFO/HaplotypeScore,INFO/InbreedingCoeff,INFO/Intervar,INFO/Intervar_STATUS,INFO/MLEAC,INFO/MLEAF,INFO/MQ,INFO/MQRankSum,INFO/NEGATIVE_TRAIN_SITE,INFO/OLD_VARIANT,INFO/POSITIVE_TRAIN_SITE,INFO/QD,INFO/RAW_MQ,INFO/ReadPosRankSum,INFO/SOR,INFO/VQSLOD,INFO/culprit,INFO/gnomad_3_1_1_AC,INFO/gnomad_3_1_1_AC_controls_and_biobanks,INFO/gnomad_3_1_1_AC_popmax,INFO/gnomad_3_1_1_AF,INFO/gnomad_3_1_1_AF_controls_and_biobanks,INFO/gnomad_3_1_1_AF_non_cancer,INFO/gnomad_3_1_1_AF_popmax,INFO/gnomad_3_1_1_AN,INFO/gnomad_3_1_1_AN_controls_and_biobanks,INFO/gnomad_3_1_1_AN_popmax,INFO/gnomad_3_1_1_nhomalt,INFO/gnomad_3_1_1_nhomalt_popmax,INFO/gnomad_3_1_1_primate_ai_score,INFO/gnomad_3_1_1_splice_ai_consequence`
+    - `include_expression`: Filters DNA vcf for high quality variants. Current recommended:
+      - Trio called VCF: `STRLEN(REF)<=50 && STRLEN(ALT)<=50 && FILTER="PASS" && GT="alt"`
+      - Single sample VCF:  `STRLEN(REF)<=50 && STRLEN(ALT)<=50 && FILTER="PASS"`
+   - `subtract_bed`: Recommend to filter regions from repeat and low complexity regions. Recommend obtaining repeat-masker bed file from UCSC, run bedtools sort + merge to simplify. Removes variant calls from `input_vcf` from notoriously difficult regions
+   - `vcf_sample_name`: **If input is trio**, provide the patient sample name to ensure desired `include_expression` is applied to the specific patient
+   - `genome_dirname`: Output dirname. Recommend STAR_{version}\_GENCODE\_{version num}_{Patient/sample id}
+   - `genome_fa`: Should match input used for DNA. For KF/INCLUDE, recommend `Homo_sapiens_assembly38_noALT_noHLA_noDecoy.fasta`.
+   - `genomeTransformType`: `Diploid`, set by default
+   - `gtf`: Recommend `PRI` assembly from [GENCODE version 45](https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_45/gencode.v45.primary_assembly.annotation.gtf.gz) for CFDE
+   - `sjdbOverhang`: Default is 100. Normally fine as-is, but for PG should probably just set it to read length minus 1
+   ### STAR aligner
+    - `reads1`: BAM/CRAM/FASTQ reads input. If BAM/CRAM workflow will convert to FASTQ. If FASTQ, read 1 file would go here
+    - `reads2`: If FASTQ and paired end, mates file, aka read 2 goes here
+    - `cram_reference`: If input reads are CRAM, provide alignment FASTA reference used for it here
+    - `outSAMattrRGline`: Output alignment read group. With **_tabs separating the tags_**, format is: ID:sample_name LB:aliquot_id PL:platform SM:BSID for example ID:7316-242 LB:750189 PL:ILLUMINA SM:BS_W72364MN
+    - `genomeDir`: If pre-built tar-gzipped PG exists, provide here to skip STAR Genome step
+  ### RSEM
+   - `wf_strand_param`: Strandedness of input reads. Default is `rf-stranded`. Use 'default' for unstranded/auto, 'rf-stranded' if read1 in the fastq read pairs is reverse complement to the transcript, 'fr-stranded' if read1 same sense as transcript
+   - `RSEMgenome`: RSEM reference tar ball.
+  ## OUTPUTS
+   - `star_ref`: If existing `genomeDir` tar ball was not provided as well as `genome_dirname` was given, workflow will have created and provided the patient's PG. This can be re-used in the event a user wants to align another sample frm the patient and/or try different aligner parameters
+   - `debug_log`: Log output from STAR GEnome Generate 
+   - `STAR_sorted_genomic_cram`: Aligned reads to genome in CRAM format
+   - `STAR_transcriptome_bam`: Typically not kept as it's seldom re-used, given that this is in beta phase, we'll keep this
+   - `STAR_gene_count`: Gene counts from STAR
+   - `STAR_junctions_out`: STAR junctions file
+   - `STAR_final_log`: STAR metrics log file of unique, multi-mapping, unmapped, and chimeric reads
+   - `RSEM_isoform` RSEM isoform expression estimates
+   - `RSEM_gene`: RSEM gene expression estimates
+
+  ## Filtering and Input Appendix
+  ### Input creation
+   - `genome_fa` was generated by first downloading the [complete hg38 fasta](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta) from Broad, then creating a chr1-22,X,Y,M chromosome list, and running the following commands to get the fasta file and index: 
+     ```sh
+     samtools faidx Homo_sapiens_assembly38.fasta -r chr_list.txt > Homo_sapiens_assembly38_noALT_noHLA_noDecoy.fasta
+     samtools faidx Homo_sapiens_assembly38_noALT_noHLA_noDecoy.fasta
+     ```
+   - `subtract_bed` was generated by navigating to https://genome.ucsc.edu/cgi-bin/hgTables, then set the following:
+     - **group**: `Repeats`
+     - **track**: `RepeatMasker`
+     - **output format**: `BED`
+     - Result was then piped to `bedtools sort | bedtools merge | gzip > rpt_merge_sort.bed.gz` 
+  ### VCF filtering
+  #### Trio VCFS
+  Two main sources of soft `FILTER` are added during creation using [this workflow](https://github.com/kids-first/kf-jointgenotyping-workflow/blob/v2.4.0/README.md):
+   - Adding tranches during VQSR
+   - Adding `lowGQ` filter `GQ < 20.0`
+  These variants get removed during bcftools step of filtering on `PASS`
+  ### Single sample VCFS
+  These have even more `FILTER` added that are dropped on `PASS`:
+   - Common
+     - ExcessHet: `ExcessHet > 54.69`
+     - QD2: `QD < 2.0`
+     - QUAL30: `QUAL < 30.0`
+   - SNP only:
+     - SOR3_SNP: `SOR > 3.0`
+     - FS60_SNP: `FS > 60.0`
+     - MQ40_SNP: `MQ < 40.0`
+     - MQRankSum-12.5_SNP: `MQRankSum < -12.5`
+     - ReadPosRankSum-8_SNP: `ReadPosRankSum < -8.0`
+   - INDEL only:
+     - QD2: `QD < 2.0`
+     - QUAL30: `QUAL < 30.0`
+     - FS200_INDEL: `FS > 200.0`
+     - ReadPosRankSum-20_INDEL: `ReadPosRankSum < -20.0`
+  ### Broad joint cohort calls
+  Provided by our collaborators at Broad, these are recommended for joint cohort calls:
+   - Genotype-quality (GQ): filter out genotypes with a quality below this threshold. Default: 20 - 
+   - Allelic-balance: filter out genotypes with allelic balance outside of [1-{allelic-balance}, {allelic-balance}]. Default: 0.8 - 
+   - Missingness-threshold: filter out variants with missingness above this threshold. Default: 0.02 - 
+   - HWE N-individuals: minimum number of individuals within a subpopulation to perform HWE test. Default: 100 - 
+   - HWE: the autosomal (or non-pseudoautosomal X in females only) site failed Hardy-Weinberg equilibrium expectations in (sub)population(s). Minimum acceptable p-value for HWE: Default: 1e-8 - 
+   - hmiss pval-threshold: minimum acceptable p-value for hmiss: Default: 1e-8 - 
+   - Sample-blacklist: list of samples to exclude. - 
+   - ExcessHet (excess of heterozygosity):filter out variants > 54.69 - 
+   - LCR (low-complexity regions): filter out variants in low-complexity regions - 
+   - Monomorphic alleles: filter out monomorphic alleles (0/0) - 
+   - VQSR: Variant Quality Score Recalibration. It is a sophisticated filtering technique applied on the variant callset that uses machine learning to model the technical profile of variants in a training set and uses that to filter out probable artifacts from the callset. We remove variants with VQSR filter. - 
+   - Use LCR-hg38-noHLA.interval_list to filter out calls in those regions
+
 
 requirements:
 - class: MultipleInputFeatureRequirement
@@ -13,189 +133,164 @@ requirements:
 inputs:
   # Strip, subset and PASS vars
   input_vcf: {type: 'File?', secondaryFiles: ['.tbi']}
-  reference_fasta: {type: 'File?', doc: "GRCh38.primary_assembly.genome.fa", "sbg:suggestedValue": {
-      class: File, path: 5f500135e4b0370371c051b4, name: GRCh38.primary_assembly.genome.fa,
-      secondaryFiles: [{class: File, path: 62866da14d85bc2e02ba52db, name: GRCh38.primary_assembly.genome.fa.fai}]},
+  reference_fasta: {type: 'File?', doc: "GRCh38.primary_assembly.genome.fa", "sbg:suggestedValue": {class: File, path: 5f500135e4b0370371c051b4,
+      name: GRCh38.primary_assembly.genome.fa, secondaryFiles: [{class: File, path: 62866da14d85bc2e02ba52db, name: GRCh38.primary_assembly.genome.fa.fai}]},
     secondaryFiles: ['.fai']}
-  strip_info: {type: 'string?', doc: "If given, remove previous annotation information based on INFO file, i.e. to strip VEP info, use INFO/ANN",
-    default: "INFO/CLNDISDB,INFO/CLNDISDBINCL,INFO/CLNDN,INFO/CLNDNINCL,INFO/CLNHGVS,INFO/CLNREVSTAT,INFO/CLNSIG,INFO/CLNSIGCONF,INFO/CLNSIGINCL,INFO/CLNVC,INFO/CLNVCSO,INFO/CLNVI,INFO/CSQ,INFO/ClippingRankSum,INFO/DB,INFO/DP,INFO/DS,INFO/END,INFO/ExcessHet,INFO/FS,INFO/HaplotypeScore,INFO/InbreedingCoeff,INFO/Intervar,INFO/Intervar_STATUS,INFO/MLEAC,INFO/MLEAF,INFO/MQ,INFO/MQRankSum,INFO/NEGATIVE_TRAIN_SITE,INFO/OLD_VARIANT,INFO/POSITIVE_TRAIN_SITE,INFO/QD,INFO/RAW_MQ,INFO/ReadPosRankSum,INFO/SOR,INFO/VQSLOD,INFO/culprit,INFO/gnomad_3_1_1_AC,INFO/gnomad_3_1_1_AC_controls_and_biobanks,INFO/gnomad_3_1_1_AC_popmax,INFO/gnomad_3_1_1_AF,INFO/gnomad_3_1_1_AF_controls_and_biobanks,INFO/gnomad_3_1_1_AF_non_cancer,INFO/gnomad_3_1_1_AF_popmax,INFO/gnomad_3_1_1_AN,INFO/gnomad_3_1_1_AN_controls_and_biobanks,INFO/gnomad_3_1_1_AN_popmax,INFO/gnomad_3_1_1_nhomalt,INFO/gnomad_3_1_1_nhomalt_popmax,INFO/gnomad_3_1_1_primate_ai_score,INFO/gnomad_3_1_1_splice_ai_consequence"}
-  output_basename: {type: 'string?', doc: "String to use as basename for outputs.
-      Will use read1 file basename if null"}
-  sample_name: {type: 'string?', doc: "Sample ID of the input reads. If not provided,
-      will use reads1 file basename."}
-  include_expression: { type: 'string?', doc: "Prefilter data frem VCF file before personal genome gen", default: STRLEN(REF)<=50 && STRLEN(ALT)<=50 && FILTER="PASS"}
-  subtract_bed: {type: 'File?', doc: "Supply if you want to remove regions for any reason, like low complexity or repeat mask, etc" }
-  vcf_sample_name: { type: 'string?', doc: "csv string of samples if user wishes to apply filtering to and output specific samples"}
+  strip_info: {type: 'string?', doc: "If given, remove previous annotation information based on INFO file, i.e. to strip VEP info,
+      use INFO/ANN", default: "INFO/CLNDISDB,INFO/CLNDISDBINCL,INFO/CLNDN,INFO/CLNDNINCL,INFO/CLNHGVS,INFO/CLNREVSTAT,INFO/CLNSIG,INFO/CLNSIGCONF,INFO/CLNSIGINCL,INFO/CLNVC,INFO/CLNVCSO,INFO/CLNVI,INFO/CSQ,INFO/ClippingRankSum,INFO/DB,INFO/DP,INFO/DS,INFO/END,INFO/ExcessHet,INFO/FS,INFO/HaplotypeScore,INFO/InbreedingCoeff,INFO/Intervar,INFO/Intervar_STATUS,INFO/MLEAC,INFO/MLEAF,INFO/MQ,INFO/MQRankSum,INFO/NEGATIVE_TRAIN_SITE,INFO/OLD_VARIANT,INFO/POSITIVE_TRAIN_SITE,INFO/QD,INFO/RAW_MQ,INFO/ReadPosRankSum,INFO/SOR,INFO/VQSLOD,INFO/culprit,INFO/gnomad_3_1_1_AC,INFO/gnomad_3_1_1_AC_controls_and_biobanks,INFO/gnomad_3_1_1_AC_popmax,INFO/gnomad_3_1_1_AF,INFO/gnomad_3_1_1_AF_controls_and_biobanks,INFO/gnomad_3_1_1_AF_non_cancer,INFO/gnomad_3_1_1_AF_popmax,INFO/gnomad_3_1_1_AN,INFO/gnomad_3_1_1_AN_controls_and_biobanks,INFO/gnomad_3_1_1_AN_popmax,INFO/gnomad_3_1_1_nhomalt,INFO/gnomad_3_1_1_nhomalt_popmax,INFO/gnomad_3_1_1_primate_ai_score,INFO/gnomad_3_1_1_splice_ai_consequence"}
+  output_basename: {type: 'string?', doc: "String to use as basename for outputs. Will use read1 file basename if null"}
+  sample_name: {type: 'string?', doc: "Sample ID of the input reads. If not provided, will use reads1 file basename."}
+  include_expression: {type: 'string?', doc: "Prefilter data frem VCF file before personal genome gen", default: STRLEN(REF)<=50 &&
+      STRLEN(ALT)<=50 && FILTER="PASS"}
+  subtract_bed: {type: 'File?', doc: "Supply if you want to remove regions for any reason, like low complexity or repeat mask, etc"}
+  vcf_sample_name: {type: 'string?', doc: "csv string of samples if user wishes to apply filtering to and output specific samples"}
   # Genome gen vars
-  genome_dirname: { type: 'string?', doc: "Output dirname. Recommend STAR_{version}_GENCODE{version num}_{Patient/sample id}. Use when PG needs to be run" }
-  genome_fa: { type: 'File?', doc: "Fasta file to index. Recommend from GENCODE, PRI assembly. Must unzip first if compressed" }
-  genomeTransformType: { type: [ 'null', {type: enum, name: genomeTransformType, symbols: [
-      "None",
-      "Haploid",
-      "Diploid"
-      ]}],
-      default: Diploid,
-      doc: "type of genome transformation - None: no transformation. Haploid: eplace reference alleles with alternative alleles from VCF file (e.g. consensus allele) \
-      Diploid: create two haplotypes for each chromosome listed in VCF file, for genotypes 1—2, assumes perfect phasing (e.g. personal genome)" }
-  gtf: { type: 'File?', doc: "Matched GTF file to index. Recommend from GENCODE, PRI assembly" }
-  runThreadN: { type: 'int?', default: 32 }
-  memory: { type: 'int?', doc: "Mem in GB required. With no VCF, 60GB is fine, need more with VCF", default: 96}
-  sjdbOverhang: { type: 'int?', default: 100, doc: "Ideal value is read len minus 1, but default 100 ok for most cases" }
+  genome_dirname: {type: 'string?', doc: "Output dirname. Recommend STAR_{version}_GENCODE{version num}_{Patient/sample id}. Use when
+      PG needs to be run"}
+  genome_fa: {type: 'File?', doc: "Fasta file to index. Recommend from GENCODE, PRI assembly. Must unzip first if compressed"}
+  genomeTransformType: {type: ['null', {type: enum, name: genomeTransformType, symbols: ["None", "Haploid", "Diploid"]}], default: Diploid,
+    doc: "type of genome transformation - None: no transformation. Haploid: eplace reference alleles with alternative alleles from
+      VCF file (e.g. consensus allele) Diploid: create two haplotypes for each chromosome listed in VCF file, for genotypes 1—2, assumes
+      perfect phasing (e.g. personal genome)"}
+  gtf: {type: 'File?', doc: "Matched GTF file to index. Recommend from GENCODE, PRI assembly"}
+  runThreadN: {type: 'int?', default: 32}
+  memory: {type: 'int?', doc: "Mem in GB required. With no VCF, 60GB is fine, need more with VCF", default: 96}
+  sjdbOverhang: {type: 'int?', default: 100, doc: "Ideal value is read len minus 1, but default 100 ok for most cases"}
   # Cutadapt 
-  r1_adapter: {type: 'string?', doc: "Optional input. If the input reads have already
-      been trimmed, leave these as null. If they do need trimming, supply the adapters."}
-  r2_adapter: {type: 'string?', doc: "Optional input. If the input reads have already
-      been trimmed, leave these as null. If they do need trimming, supply the adapters."}
-  min_len: {type: 'int?', doc: "If you do not use this option, reads that have a length
-      of zero (empty reads) are kept in the output", default: 20}
+  r1_adapter: {type: 'string?', doc: "Optional input. If the input reads have already been trimmed, leave these as null. If they do
+      need trimming, supply the adapters."}
+  r2_adapter: {type: 'string?', doc: "Optional input. If the input reads have already been trimmed, leave these as null. If they do
+      need trimming, supply the adapters."}
+  min_len: {type: 'int?', doc: "If you do not use this option, reads that have a length of zero (empty reads) are kept in the output",
+    default: 20}
   quality_base: {type: 'int?', doc: "Phred scale used", default: 33}
   quality_cutoff: {type: 'int[]?', doc: "Quality trim cutoff, see https://cutadapt.readthedocs.io/en/v3.4/guide.html#quality-trimming
       for how 5' 3' is handled"}
   # STAR Diploid Align Vars
-  reads1: {type: File, doc: "Input fastq file, gzipped or uncompressed OR alignment
-      file"}
+  reads1: {type: File, doc: "Input fastq file, gzipped or uncompressed OR alignment file"}
   reads2: {type: 'File?', doc: "If paired end, R2 reads files, gzipped or uncompressed"}
-  samtools_fastq_cores: {type: 'int?', doc: "Num cores for align2fastq conversion,
-      if input is an alignment file", default: 16}
-  cram_reference: {type: 'File?', secondaryFiles: [.fai], doc: "If input align is
-      cram and you are uncertain all contigs are registered at http://www.ebi.ac.uk/ena/cram/md5/,
-      provide here"}
-  outSAMattrRGline: { type: string, doc: "Suggested setting, with TABS SEPARATING \
-      THE TAGS, format is: ID:sample_name LB:aliquot_id PL:platform SM:BSID for \
-      example ID:7316-242 LB:750189 PL:ILLUMINA SM:BS_W72364MN"}
-  genomeDir: { type: 'File?', doc: "Tar gzipped reference that will be unzipped at run time. Provide to skip genome generate" }
-  twopassMode: { type: ['null', {type: enum, name: twopassMode, symbols: ["Basic", "None"]}], default: "Basic",
-  doc: "Enable two pass mode to detect novel splice events. Default is basic (on)."}
-  alignSJoverhangMin: { type: 'int?', default: 8, doc: "minimum overhang for unannotated junctions. ENCODE default used."}
-  outFilterMismatchNoverLmax: { type: 'float?', default: 0.1, doc: "alignment will be output only if its ratio of mismatches to *mapped* \
-  length is less than or equal to this value"}
-  outFilterType: { type: [ 'null', {type: enum, name: outFilterType, symbols: ["BySJout", "Normal"]}], default: "BySJout",
-  doc: "type of filtering. Normal: standard filtering using only current alignment. BySJout (default): keep only those reads that contain junctions \
-  that passed filtering into SJ.out.tab."}
-  outFilterScoreMinOverLread: { type: 'float?', default: 0.33, doc: "alignment will be output only if its score is higher than or equal to this value, \
-  normalized to read length (sum of mate's lengths for paired-end reads)"}
-  outFilterMatchNminOverLread: { type: 'float?', default: 0.33, doc: "alignment will be output only if the number of matched bases is higher than or \
-  equal to this value., normalized to the read length (sum of mates' lengths for paired-end reads)"}
-  outReadsUnmapped: { type: [ 'null', {type: enum, name: outReadsUnmapped, symbols: ["None", "Fastx"]}], default: "None",
-  doc: "output of unmapped and partially mapped (i.e. mapped only one mate of a paired end read) reads in separate file(s). \
-  none (default): no output. Fastx: output in separate fasta/fastq files, Unmapped.out.mate1/2."}
-  limitSjdbInsertNsj: { type: 'int?', default: 1200000, doc: "maximum number of junction to be inserted to the genome on the fly \
-  at the mapping stage, including those from annotations and those detected in the 1st step of the 2-pass run"}
-  outSAMstrandField: { type: [ 'null', {type: enum, name: outSAMstrandField, symbols: ["intronMotif", "None"]}], default: "intronMotif",
-  doc: "Cufflinks-like strand field flag. None: not used. intronMotif (default): strand derived from the intron motif. This option changes the output \
-  alignments: reads with inconsistent and/or non-canonical introns are filtered out."}
-  outFilterIntronMotifs: { type: [ 'null', {type: enum, name: outFilterIntronMotifs, symbols: ["None", "RemoveNoncanonical", "RemoveNoncanonicalUnannotated"]}],
-  default: "None",
-  doc: "filter alignment using their motifs. None (default): no filtering. RemoveNoncanonical: filter out alignments that contain non-canonical junctions \
-  RemoveNoncanonicalUnannotated: filter out alignments that contain non-canonical unannotated junctions when using annotated splice junctions database. \
-  The annotated non-canonical junctions will be kept."}
-  alignSoftClipAtReferenceEnds:  { type: [ 'null', {type: enum, name: alignSoftClipAtReferenceEnds, symbols: ["Yes", "No"]}], default: "Yes",
-  doc: "allow the soft-clipping of the alignments past the end of the chromosomes. Yes (default): allow. \
-  No: prohibit, useful for compatibility with Cufflinks"}
-  quantMode: { type: [ 'null', {type: enum, name: quantMode, symbols: [TranscriptomeSAM GeneCounts, -, TranscriptomeSAM, GeneCounts]}],
-  default: TranscriptomeSAM GeneCounts,
-  doc: "types of quantification requested. -: none. TranscriptomeSAM: output SAM/BAM alignments to transcriptome into a separate file \
-  GeneCounts: count reads per gene. Choices are additive, so default is 'TranscriptomeSAM GeneCounts'"}
-  quantTranscriptomeSAMoutput: { type: [ 'null', {type: enum, name: quantTranscriptomeSAMoutput, symbols: [BanSingleEnd_BanIndels_ExtendSoftclip, BanSingleEnd, BanSingleEnd_ExtendSoftclip]}],
-  default: BanSingleEnd_ExtendSoftclip,
-  doc: "alignment filtering for TranscriptomeSAM output"}
-  outSAMtype: { type: [ 'null', {type: enum, name: outSAMtype, symbols: ["BAM Unsorted", "None", "BAM SortedByCoordinate", "SAM Unsorted", "SAM SortedByCoordinate"]}],
-  default: "BAM Unsorted",
-  doc: "type of SAM/BAM output. None: no SAM/BAM output. Otherwise, first word is output type (BAM or SAM), second is sort type (Unsorted or SortedByCoordinate)"}
-  outSAMunmapped: { type: [ 'null', {type: enum, name: outSAMunmapped, symbols: ["Within", "None", "Within KeepPairs"]}],
-  default: "Within",
-  doc: "output of unmapped reads in the SAM format. None: no output. Within (default): output unmapped reads within the main SAM file (i.e. Aligned.out.sam) \
-  Within KeepPairs: record unmapped mate for each alignment, and, in case of unsorted output, keep it adjacent to its mapped mate. Only affects \
-  multi-mapping reads"}
-  genomeTransformOutput: { type: [ 'null', {type: enum, name: quantMode, symbols: [None, SAM, SJ, Quant, SAM SJ, SAM Quant, SAM SJ Quant, SJ Quant ]}],
-  default: "SAM SJ Quant",
-  doc: "which output to transform back to original genome"}
-  genomeLoad: { type: [ 'null', {type: enum, name: genomeLoad, symbols: ["NoSharedMemory", "LoadAndKeep", "LoadAndRemove", "LoadAndExit"]}],
-  default: "NoSharedMemory",
-  doc: "mode of shared memory usage for the genome file. In this context, the default value makes the most sense, the others are their as a courtesy."}
-  chimMainSegmentMultNmax: { type: 'int?', doc: "maximum number of multi-alignments for the main chimeric segment. =1 will prohibit multimapping main segments"}
-  outSAMattributes: { type: 'string?', default: "NH HI AS nM NM MD ha", doc: "a string of desired SAM attributes, in the order desired for the output SAM. Tags can be listed in any combination/order. \
-  Please refer to the STAR manual, as there are numerous combinations: https://raw.githubusercontent.com/alexdobin/STAR/master/doc/STARmanual.pdf"}
+  samtools_fastq_cores: {type: 'int?', doc: "Num cores for align2fastq conversion, if input is an alignment file", default: 16}
+  cram_reference: {type: 'File?', secondaryFiles: [.fai], doc: "If input align is cram and you are uncertain all contigs are registered
+      at http://www.ebi.ac.uk/ena/cram/md5/, provide here"}
+  outSAMattrRGline: {type: string, doc: "Suggested setting, with TABS SEPARATING THE TAGS, format is: ID:sample_name LB:aliquot_id
+      PL:platform SM:BSID for example ID:7316-242 LB:750189 PL:ILLUMINA SM:BS_W72364MN"}
+  genomeDir: {type: 'File?', doc: "Tar gzipped reference that will be unzipped at run time. Provide to skip genome generate"}
+  twopassMode: {type: ['null', {type: enum, name: twopassMode, symbols: ["Basic", "None"]}], default: "Basic", doc: "Enable two pass
+      mode to detect novel splice events. Default is basic (on)."}
+  alignSJoverhangMin: {type: 'int?', default: 8, doc: "minimum overhang for unannotated junctions. ENCODE default used."}
+  outFilterMismatchNoverLmax: {type: 'float?', default: 0.1, doc: "alignment will be output only if its ratio of mismatches to *mapped*
+      length is less than or equal to this value"}
+  outFilterType: {type: ['null', {type: enum, name: outFilterType, symbols: ["BySJout", "Normal"]}], default: "BySJout", doc: "type
+      of filtering. Normal: standard filtering using only current alignment. BySJout (default): keep only those reads that contain
+      junctions that passed filtering into SJ.out.tab."}
+  outFilterScoreMinOverLread: {type: 'float?', default: 0.33, doc: "alignment will be output only if its score is higher than or equal
+      to this value, normalized to read length (sum of mate's lengths for paired-end reads)"}
+  outFilterMatchNminOverLread: {type: 'float?', default: 0.33, doc: "alignment will be output only if the number of matched bases
+      is higher than or equal to this value., normalized to the read length (sum of mates' lengths for paired-end reads)"}
+  outReadsUnmapped: {type: ['null', {type: enum, name: outReadsUnmapped, symbols: ["None", "Fastx"]}], default: "None", doc: "output
+      of unmapped and partially mapped (i.e. mapped only one mate of a paired end read) reads in separate file(s). none (default):
+      no output. Fastx: output in separate fasta/fastq files, Unmapped.out.mate1/2."}
+  limitSjdbInsertNsj: {type: 'int?', default: 1200000, doc: "maximum number of junction to be inserted to the genome on the fly at
+      the mapping stage, including those from annotations and those detected in the 1st step of the 2-pass run"}
+  outSAMstrandField: {type: ['null', {type: enum, name: outSAMstrandField, symbols: ["intronMotif", "None"]}], default: "intronMotif",
+    doc: "Cufflinks-like strand field flag. None: not used. intronMotif (default): strand derived from the intron motif. This option
+      changes the output alignments: reads with inconsistent and/or non-canonical introns are filtered out."}
+  outFilterIntronMotifs: {type: ['null', {type: enum, name: outFilterIntronMotifs, symbols: ["None", "RemoveNoncanonical", "RemoveNoncanonicalUnannotated"]}],
+    default: "None", doc: "filter alignment using their motifs. None (default): no filtering. RemoveNoncanonical: filter out alignments
+      that contain non-canonical junctions RemoveNoncanonicalUnannotated: filter out alignments that contain non-canonical unannotated
+      junctions when using annotated splice junctions database. The annotated non-canonical junctions will be kept."}
+  alignSoftClipAtReferenceEnds: {type: ['null', {type: enum, name: alignSoftClipAtReferenceEnds, symbols: ["Yes", "No"]}], default: "Yes",
+    doc: "allow the soft-clipping of the alignments past the end of the chromosomes. Yes (default): allow. No: prohibit, useful for
+      compatibility with Cufflinks"}
+  quantMode: {type: ['null', {type: enum, name: quantMode, symbols: [TranscriptomeSAM GeneCounts, '-', TranscriptomeSAM, GeneCounts]}],
+    default: TranscriptomeSAM GeneCounts, doc: "types of quantification requested. -: none. TranscriptomeSAM: output SAM/BAM alignments
+      to transcriptome into a separate file GeneCounts: count reads per gene. Choices are additive, so default is 'TranscriptomeSAM
+      GeneCounts'"}
+  quantTranscriptomeSAMoutput: {type: ['null', {type: enum, name: quantTranscriptomeSAMoutput, symbols: [BanSingleEnd_BanIndels_ExtendSoftclip,
+          BanSingleEnd, BanSingleEnd_ExtendSoftclip]}], default: BanSingleEnd_ExtendSoftclip, doc: "alignment filtering for TranscriptomeSAM
+      output"}
+  outSAMtype: {type: ['null', {type: enum, name: outSAMtype, symbols: ["BAM Unsorted", "None", "BAM SortedByCoordinate", "SAM Unsorted",
+          "SAM SortedByCoordinate"]}], default: "BAM Unsorted", doc: "type of SAM/BAM output. None: no SAM/BAM output. Otherwise,
+      first word is output type (BAM or SAM), second is sort type (Unsorted or SortedByCoordinate)"}
+  outSAMunmapped: {type: ['null', {type: enum, name: outSAMunmapped, symbols: ["Within", "None", "Within KeepPairs"]}], default: "Within",
+    doc: "output of unmapped reads in the SAM format. None: no output. Within (default): output unmapped reads within the main SAM
+      file (i.e. Aligned.out.sam) Within KeepPairs: record unmapped mate for each alignment, and, in case of unsorted output, keep
+      it adjacent to its mapped mate. Only affects multi-mapping reads"}
+  genomeTransformOutput: {type: ['null', {type: enum, name: quantMode, symbols: [None, SAM, SJ, Quant, SAM SJ, SAM Quant, SAM SJ Quant,
+          SJ Quant]}], default: "SAM SJ Quant", doc: "which output to transform back to original genome"}
+  genomeLoad: {type: ['null', {type: enum, name: genomeLoad, symbols: ["NoSharedMemory", "LoadAndKeep", "LoadAndRemove", "LoadAndExit"]}],
+    default: "NoSharedMemory", doc: "mode of shared memory usage for the genome file. In this context, the default value makes the
+      most sense, the others are their as a courtesy."}
+  chimMainSegmentMultNmax: {type: 'int?', doc: "maximum number of multi-alignments for the main chimeric segment. =1 will prohibit
+      multimapping main segments"}
+  outSAMattributes: {type: 'string?', default: "NH HI AS nM NM MD ha", doc: "a string of desired SAM attributes, in the order desired
+      for the output SAM. Tags can be listed in any combination/order. Please refer to the STAR manual, as there are numerous combinations:
+      https://raw.githubusercontent.com/alexdobin/STAR/master/doc/STARmanual.pdf"}
   # fusion specific
-  alignInsertionFlush: { type: [ 'null', {type: enum, name: alignInsertionFlush, symbols: ["None", "Right"]}], default: "None",
-  doc: "how to flush ambiguous insertion positions. None (default): insertions not flushed. Right: insertions flushed to the right.
-  STAR Fusion recommended (SF)"}
-  alignIntronMax: { type: 'int?', default: 1000000, doc: "maximum intron size. SF recommends 100000"}
-  alignMatesGapMax: { type: 'int?', default: 1000000, doc: "maximum genomic distance between mates, SF recommends 100000 \
-  to avoid readthru fusions within 100k"}
-  alignSJDBoverhangMin: { type: 'int?', default: 1, doc: "minimum overhang for annotated junctions. SF recommends 10"}
-  outFilterMismatchNmax: { type: 'int?', default: 999,  doc: "maximum number of mismatches per pair, large number switches off this filter"}
-  alignSJstitchMismatchNmax: { type: 'string?', default: "0 -1 0 0", doc: "maximum number of mismatches for stitching of the splice junctions. \
-  Value '5 -1 5 5' improves SF chimeric junctions, also recommended by arriba (AR)"}
-  alignSplicedMateMapLmin: { type: 'int?', default: 0, doc: "minimum mapped length for a read mate that is spliced. SF recommends 30"}
-  alignSplicedMateMapLminOverLmate: { type: 'float?', default: 0.66,
-  doc: "alignSplicedMateMapLmin normalized to mate length. SF recommends 0, AR 0.5"}
-  chimJunctionOverhangMin: { type: 'int?', doc: "minimum overhang for a chimeric junction. SF recommends 8, AR 10"}
-  chimMultimapNmax: { type: 'int?', default: 0, doc: "maximum number of chimeric multi-alignments. SF recommends 20, AR 50."}
-  chimMultimapScoreRange: { type: 'int?', default: 1, doc: "the score range for multi-mapping chimeras below the best chimeric \
-  score. Only works with chimMultimapNmax > 1. SF recommends 3"}
-  chimNonchimScoreDropMin: { type: 'int?', default: 20,
-  doc: "int>=0: to trigger chimeric detection, the drop in the best non-chimeric \
-  alignment score with respect to the read length has to be greater than this value. SF recommends 10"}
-  chimOutJunctionFormat: { type: 'int?', default: 1, doc: "formatting type for the Chimeric.out.junction file, value 1 REQUIRED for SF"}
-  chimOutType: { type: [ 'null', {type: enum, name: chimOutType, symbols: [
-      "Junctions SeparateSAMold WithinBAM SoftClip",
-      "Junctions", "SeparateSAMold",
-      "WithinBAM SoftClip",
-      "WithinBAM HardClip",
-      "Junctions SeparateSAMold",
-      "Junctions WithinBAM SoftClip",
-      "Junctions WithinBAM HardClip",
-      "Junctions SeparateSAMold WithinBAM HardClip",
-      "SeparateSAMold WithinBAM SoftClip",
-      "SeparateSAMold WithinBAM HardClip"
-      ]}],
-  doc: "type of chimeric output. Args are additive, and defined as such - Junctions: Chimeric.out.junction. SeparateSAMold: output old SAM into separate Chimeric.out.sam file \
-  WithinBAM: output into main aligned BAM files (Aligned.*.bam). WithinBAM HardClip: hard-clipping in the CIGAR for supplemental chimeric alignments \
-  WithinBAM SoftClip:soft-clipping in the CIGAR for supplemental chimeric alignments"}
-  chimScoreDropMax: { type: 'int?', default: 20,
-  doc: "max drop (difference) of chimeric score (the sum of scores of all chimeric segments) from the read length. AR recommends 30"}
-  chimScoreJunctionNonGTAG: { type: 'int?', default: -1, doc: "penalty for a non-GT/AG chimeric junction. \
-  default -1, SF recommends -4, AR -1"}
-  chimScoreSeparation: { type: 'int?', default: 10,
-  doc: "int>=0: minimum difference (separation) between the best chimeric score and the next one. AR recommends 1"}
-  chimSegmentMin: { type: 'int?', doc: "minimum length of chimeric segment length, if ==0, no chimeric output. \
-  REQUIRED for SF, 12 is their default, AR recommends 10", default: 0 }
-  chimSegmentReadGapMax: { type: 'int?', default: 0, doc: "maximum gap in the read sequence between chimeric segments. AR recommends 3"}
-  outFilterMultimapNmax: { type: 'int?', default: 20, doc: "max number of multiple alignments allowed for \
-  a read: if exceeded, the read is considered unmapped. ENCODE value is default. AR recommends 50"}
-  peOverlapMMp: { type: 'float?', default: 0.01, doc: "maximum proportion of mismatched bases in the overlap area. SF recommends 0.1"}
-  peOverlapNbasesMin: { type: 'int?', default: 0,
-  doc: "minimum number of overlap bases to trigger mates merging and realignment. Specify >0 value to switch \
-  on the 'merging of overlapping mates'algorithm. SF recommends 12,  AR recommends 10"}
-  winAnchorMultimapNmax: { type: 'int?', default: 100,
-  doc: "max number of loci anchors are allowed to map to"}
-  wf_strand_param: {type: ['null', {type: 'enum', name: wf_strand_param, symbols: [
-          "default", "rf-stranded", "fr-stranded"]}], doc: "use 'default' for unstranded/auto,
-      'rf-stranded' if read1 in the fastq read pairs is reverse complement to the
-      transcript, 'fr-stranded' if read1 same sense as transcript",
-      default: "rf-stranded"}
-  RSEMgenome: {type: 'File', doc: "RSEM reference tar ball", "sbg:suggestedValue": {
-      class: File, path: 62853e7ad63f7c6d8d7ae5a5, name: RSEM_GENCODE39.tar.gz}}
-  estimate_rspd: {type: 'boolean?', doc: "Set this option if you want to estimate
-      the read start position distribution (RSPD) from data", default: true}
+  alignInsertionFlush: {type: ['null', {type: enum, name: alignInsertionFlush, symbols: ["None", "Right"]}], default: "None", doc: "how
+      to flush ambiguous insertion positions. None (default): insertions not flushed. Right: insertions flushed to the right. STAR
+      Fusion recommended (SF)"}
+  alignIntronMax: {type: 'int?', default: 1000000, doc: "maximum intron size. SF recommends 100000"}
+  alignMatesGapMax: {type: 'int?', default: 1000000, doc: "maximum genomic distance between mates, SF recommends 100000 to avoid readthru
+      fusions within 100k"}
+  alignSJDBoverhangMin: {type: 'int?', default: 1, doc: "minimum overhang for annotated junctions. SF recommends 10"}
+  outFilterMismatchNmax: {type: 'int?', default: 999, doc: "maximum number of mismatches per pair, large number switches off this
+      filter"}
+  alignSJstitchMismatchNmax: {type: 'string?', default: "0 -1 0 0", doc: "maximum number of mismatches for stitching of the splice
+      junctions. Value '5 -1 5 5' improves SF chimeric junctions, also recommended by arriba (AR)"}
+  alignSplicedMateMapLmin: {type: 'int?', default: 0, doc: "minimum mapped length for a read mate that is spliced. SF recommends 30"}
+  alignSplicedMateMapLminOverLmate: {type: 'float?', default: 0.66, doc: "alignSplicedMateMapLmin normalized to mate length. SF recommends
+      0, AR 0.5"}
+  chimJunctionOverhangMin: {type: 'int?', doc: "minimum overhang for a chimeric junction. SF recommends 8, AR 10"}
+  chimMultimapNmax: {type: 'int?', default: 0, doc: "maximum number of chimeric multi-alignments. SF recommends 20, AR 50."}
+  chimMultimapScoreRange: {type: 'int?', default: 1, doc: "the score range for multi-mapping chimeras below the best chimeric score.
+      Only works with chimMultimapNmax > 1. SF recommends 3"}
+  chimNonchimScoreDropMin: {type: 'int?', default: 20, doc: "int>=0: to trigger chimeric detection, the drop in the best non-chimeric
+      alignment score with respect to the read length has to be greater than this value. SF recommends 10"}
+  chimOutJunctionFormat: {type: 'int?', default: 1, doc: "formatting type for the Chimeric.out.junction file, value 1 REQUIRED for
+      SF"}
+  chimOutType: {type: ['null', {type: enum, name: chimOutType, symbols: ["Junctions SeparateSAMold WithinBAM SoftClip", "Junctions",
+          "SeparateSAMold", "WithinBAM SoftClip", "WithinBAM HardClip", "Junctions SeparateSAMold", "Junctions WithinBAM SoftClip",
+          "Junctions WithinBAM HardClip", "Junctions SeparateSAMold WithinBAM HardClip", "SeparateSAMold WithinBAM SoftClip", "SeparateSAMold
+            WithinBAM HardClip"]}], doc: "type of chimeric output. Args are additive, and defined as such - Junctions: Chimeric.out.junction.
+      SeparateSAMold: output old SAM into separate Chimeric.out.sam file WithinBAM: output into main aligned BAM files (Aligned.*.bam).
+      WithinBAM HardClip: hard-clipping in the CIGAR for supplemental chimeric alignments WithinBAM SoftClip:soft-clipping in the
+      CIGAR for supplemental chimeric alignments"}
+  chimScoreDropMax: {type: 'int?', default: 20, doc: "max drop (difference) of chimeric score (the sum of scores of all chimeric segments)
+      from the read length. AR recommends 30"}
+  chimScoreJunctionNonGTAG: {type: 'int?', default: -1, doc: "penalty for a non-GT/AG chimeric junction. default -1, SF recommends
+      -4, AR -1"}
+  chimScoreSeparation: {type: 'int?', default: 10, doc: "int>=0: minimum difference (separation) between the best chimeric score and
+      the next one. AR recommends 1"}
+  chimSegmentMin: {type: 'int?', doc: "minimum length of chimeric segment length, if ==0, no chimeric output. REQUIRED for SF, 12
+      is their default, AR recommends 10", default: 0}
+  chimSegmentReadGapMax: {type: 'int?', default: 0, doc: "maximum gap in the read sequence between chimeric segments. AR recommends
+      3"}
+  outFilterMultimapNmax: {type: 'int?', default: 20, doc: "max number of multiple alignments allowed for a read: if exceeded, the
+      read is considered unmapped. ENCODE value is default. AR recommends 50"}
+  peOverlapMMp: {type: 'float?', default: 0.01, doc: "maximum proportion of mismatched bases in the overlap area. SF recommends 0.1"}
+  peOverlapNbasesMin: {type: 'int?', default: 0, doc: "minimum number of overlap bases to trigger mates merging and realignment. Specify
+      >0 value to switch on the 'merging of overlapping mates'algorithm. SF recommends 12,  AR recommends 10"}
+  winAnchorMultimapNmax: {type: 'int?', default: 100, doc: "max number of loci anchors are allowed to map to"}
+  wf_strand_param: {type: ['null', {type: 'enum', name: wf_strand_param, symbols: ["default", "rf-stranded", "fr-stranded"]}], doc: "use
+      'default' for unstranded/auto, 'rf-stranded' if read1 in the fastq read pairs is reverse complement to the transcript, 'fr-stranded'
+      if read1 same sense as transcript", default: "rf-stranded"}
+  RSEMgenome: {type: 'File', doc: "RSEM reference tar ball", "sbg:suggestedValue": {class: File, path: 62853e7ad63f7c6d8d7ae5a5, name: RSEM_GENCODE39.tar.gz}}
+  estimate_rspd: {type: 'boolean?', doc: "Set this option if you want to estimate the read start position distribution (RSPD) from
+      data", default: true}
 
 outputs:
-  star_ref: { type: 'File?', outputSource: star_personal_genome_generate/star_ref }
-  debug_log: { type: 'File?', outputSource: star_personal_genome_generate/debug_log }
-  STAR_sorted_genomic_cram: {type: 'File', outputSource: samtools_bam_to_cram/output,
-    doc: "STAR sorted and indexed genomic alignment cram"}
-  STAR_transcriptome_bam: { type: File, outputSource: star_2-7-11b_diploid/transcriptome_bam_out }
-  STAR_gene_count: {type: 'File', outputSource: star_2-7-11b_diploid/gene_counts, doc: "STAR
-      genecounts"}
-  STAR_junctions_out: {type: 'File', outputSource: star_2-7-11b_diploid/junctions_out, doc: "STARjunction
-      reads"}
-  STAR_final_log: {type: 'File', outputSource: star_2-7-11b_diploid/log_final_out, doc: "STAR
-      metricslog file of unique, multi-mapping, unmapped, and chimeric reads"}
-  RSEM_isoform: {type: 'File', outputSource: rsem/isoform_out, doc: "RSEM isoform
-      expression estimates"}
-  RSEM_gene: {type: 'File', outputSource: rsem/gene_out, doc: "RSEM gene expression
-      estimates"}
+  star_ref: {type: 'File?', outputSource: star_personal_genome_generate/star_ref}
+  debug_log: {type: 'File?', outputSource: star_personal_genome_generate/debug_log}
+  STAR_sorted_genomic_cram: {type: 'File', outputSource: samtools_bam_to_cram/output, doc: "STAR sorted and indexed genomic alignment
+      cram"}
+  STAR_transcriptome_bam: {type: File, outputSource: star_2-7-11b_diploid/transcriptome_bam_out}
+  STAR_gene_count: {type: 'File', outputSource: star_2-7-11b_diploid/gene_counts, doc: "STAR genecounts"}
+  STAR_junctions_out: {type: 'File', outputSource: star_2-7-11b_diploid/junctions_out, doc: "STARjunction reads"}
+  STAR_final_log: {type: 'File', outputSource: star_2-7-11b_diploid/log_final_out, doc: "STAR metricslog file of unique, multi-mapping,
+      unmapped, and chimeric reads"}
+  RSEM_isoform: {type: 'File', outputSource: rsem/isoform_out, doc: "RSEM isoform expression estimates"}
+  RSEM_gene: {type: 'File', outputSource: rsem/gene_out, doc: "RSEM gene expression estimates"}
 
 steps:
   basename_picker:
@@ -225,7 +320,7 @@ steps:
       tool_name:
         valueFrom: "dna_in"
       include_expression: include_expression
-      sample_name: vcf_sample_name  
+      sample_name: vcf_sample_name
       subtract_bed: subtract_bed
       # Genome gen vars
       genomeDir: genome_dirname
@@ -271,7 +366,7 @@ steps:
     run: ../tools/star_2.7.11b_diploid_align.cwl
     in:
       outSAMattrRGline: basename_picker/outrg
-      genomeDir: 
+      genomeDir:
         source: [star_personal_genome_generate/star_ref, genomeDir]
         pickValue: first_non_null
       readFilesIn1:
@@ -325,8 +420,7 @@ steps:
       peOverlapMMp: peOverlapMMp
       peOverlapNbasesMin: peOverlapNbasesMin
       winAnchorMultimapNmax: winAnchorMultimapNmax
-    out: [gene_counts, genomic_bam_out, junctions_out,
-      log_final_out, log_out, log_progress_out, transcriptome_bam_out]
+    out: [gene_counts, genomic_bam_out, junctions_out, log_final_out, log_out, log_progress_out, transcriptome_bam_out]
   strand_parse:
     run: ../tools/expression_parse_strand_param.cwl
     in:
@@ -376,3 +470,5 @@ $namespaces:
 hints:
 - class: "sbg:maxNumberOfParallelInstances"
   value: 3
+sbg:license: Apache License 2.0
+sbg:publisher: KFDRC