From 3eaaf70bc5ec8b6aca8c745d691488cfb77c78f9 Mon Sep 17 00:00:00 2001
From: morsecodist <todd@morsecodist.io>
Date: Wed, 1 Feb 2023 13:28:18 -0800
Subject: [PATCH 01/13] Unify host genome generation

---
 .../host_genome_generation.wdl                | 459 ++++++++++++------
 .../host-genome-generation/test/test_wdl.py   |   7 +-
 2 files changed, 317 insertions(+), 149 deletions(-)

diff --git a/workflows/host-genome-generation/host_genome_generation.wdl b/workflows/host-genome-generation/host_genome_generation.wdl
index 9398d208f..f29be4395 100644
--- a/workflows/host-genome-generation/host_genome_generation.wdl
+++ b/workflows/host-genome-generation/host_genome_generation.wdl
@@ -1,150 +1,319 @@
 version 1.1
 
-workflow index_generation {
-    input {
-        File input_fasta
-        File? input_gtf
-        String host_name
-        File ercc_fasta
-        File ercc_gtf
-        String docker_image_id
-    }
-
-    call GenerateHostGenome {
-        input:
-        input_fasta = input_fasta,
-        input_gtf = input_gtf,
-        host_name = host_name,
-        ercc_fasta = ercc_fasta,
-        ercc_gtf = ercc_gtf,
-        docker_image_id = docker_image_id
-    }
-
-    output {
-        File original_input_fasta = GenerateHostGenome.original_input_fasta
-        File? original_input_gtf = GenerateHostGenome.original_input_gtf
-        File fasta_with_ercc_fa = GenerateHostGenome.fasta_with_ercc_fa
-        File? gtf_with_ercc_gtf = GenerateHostGenome.gtf_with_ercc_gtf
-        File star_genome_tar = GenerateHostGenome.star_genome_tar
-        File bowtie_genome_tar = GenerateHostGenome.bowtie_genome_tar
-        File minimap2_dna = GenerateHostGenome.minimap2_dna
-        File minimap2_rna = GenerateHostGenome.minimap2_rna
-    }
+# Build host genome indexes for host_filter.wdl (2022 version)
+# - Bowtie2 (genome)
+# - HISAT2 (genome + splice junctions)
+# - kallisto (transcriptome)
+# - minimap2 (used not in short-read-mngs host filtering, but rather the ONT equivalent)
+# - STAR (used in old version of short-read-mngs host filtering, kept temporarily so we can support both)
+# ERCC sequences are spiked-in to all three indexes. Lastly takes an array of other spike-ins for
+# the Bowtie2 and HISAT2 indexes.
+# Warning: HISAT2 requires huge RAM to build the spliced index (>200G for human).
+#          But the index file size and aligner memory usage are relatively small.
+workflow host_filter_indexing {
+  input {
+    String genome_name
+
+    # host genomic DNA
+    File genome_fasta_gz
+    # host transcript models on the above genomic DNA (for HISAT2 spliced alignment)
+    File? transcripts_gtf_gz
+    # host transcript sequences (for kallisto)
+    Array[File] transcripts_fasta_gz = []
+
+    # ERCC sequences to spike in to the genome and transcript indexes
+    File ERCC_fasta_gz
+
+    # Additional FASTA file(s) to spike into the Bowtie2 & HISAT2 indexes (e.g. EBV, phiX)
+    # Sequence names must be unique among all FASTAs!
+    Array[File] other_fasta_gz = []
+
+    String docker
+  }
+
+  call ensure_gz as genome_fasta {
+    # accommodate uncompressed genome_fasta_gz; this makes it more convenient to use some of our
+    # existing host genome FASTAs which we archived without compression.
+    input:
+    maybe_gz = genome_fasta_gz,
+    docker
+  }
+
+  call bowtie2_build {
+    input:
+    fasta_gz = flatten([[genome_fasta.gz, ERCC_fasta_gz], other_fasta_gz]),
+    genome_name, docker
+  }
+
+  call hisat2_build {
+    input:
+    fasta_gz = flatten([[genome_fasta.gz, ERCC_fasta_gz], other_fasta_gz]),
+    transcripts_gtf_gz, genome_name, docker
+  }
+
+  call kallisto_index {
+    input:
+    transcripts_fasta_gz = flatten([transcripts_fasta_gz, [ERCC_fasta_gz]]),
+    genome_name, docker
+  }
+
+  call minimap2_index as minimap2_index_dna {
+    input:
+    fasta_gz = flatten([[genome_fasta.gz, ERCC_fasta_gz], other_fasta_gz]),
+    nucleotide_type = "dna",
+    genome_name, docker
+  }
+
+  call minimap2_index as minimap2_index_rna {
+    input:
+    fasta_gz = flatten([[genome_fasta.gz, ERCC_fasta_gz], other_fasta_gz]),
+    nucleotide_type = "rna",
+    genome_name, docker
+  }
+
+  call star_generate {
+    input:
+    fasta_gz = flatten([[genome_fasta.gz, ERCC_fasta_gz], other_fasta_gz]),
+    transcripts_gtf_gz, genome_name, docker
+  }
+
+  output {
+    File bowtie2_index_tar = bowtie2_build.index_tar
+    File hisat2_index_tar = hisat2_build.index_tar
+    File kallisto_idx = kallisto_index.idx
+    File minimap2_dna_mmi = minimap2_index_dna.index_mmi
+    File minimap2_rna_mmi = minimap2_index_rna.index_mmi
+    File star_genome_tar = star_generate.star_genome_tar
+
+    # also output the input files, to facilitate archival/provenance
+    File original_genome_fasta_gz = genome_fasta.gz
+    File? original_transcripts_gtf_gz = transcripts_gtf_gz
+    Array[File] original_transcripts_fasta_gz = transcripts_fasta_gz
+    File original_ERCC_fasta_gz = ERCC_fasta_gz
+    Array[File] original_other_fasta_gz = other_fasta_gz
+  }
+}
+
+task ensure_gz {
+  input {
+    File maybe_gz
+    String docker
+  }
+
+  String name = basename(maybe_gz)
+
+  command <<<
+    set -euxo pipefail
+    mkdir ans
+    if gzip -t '~{maybe_gz}'; then
+      cp '~{maybe_gz}' ans/
+    else
+      pigz -c -p 4 '~{maybe_gz}' > 'ans/~{name}.gz'
+    fi
+  >>>
+
+  output {
+      File gz = glob("ans/*")[0]
+  }
+
+  runtime {
+      docker: docker
+      cpu: 4
+      memory: "4GiB"
+  }
+}
+
+task bowtie2_build {
+  input {
+    Array[File] fasta_gz
+    String genome_name
+    Int seed = 42
+
+    Int cpu = 16
+    String docker
+  }
+
+  command <<<
+    set -euxo pipefail
+    TMPDIR=${TMPDIR:-/tmp}
+
+    all_fasta="$TMPDIR/all.fasta"
+    pigz -dc ~{sep(' ',fasta_gz)} > "$all_fasta"
+
+    mkdir -p "$TMPDIR"'/bt2/~{genome_name}'
+    >&2 bowtie2-build --seed ~{seed} --threads ~{cpu} "$all_fasta" "$TMPDIR"'/bt2/~{genome_name}/~{genome_name}'
+    >&2 ls -lR "$TMPDIR/bt2"
+    env -C "$TMPDIR/bt2" tar c . > '~{genome_name}.bowtie2.tar'
+  >>>
+
+  output {
+      File index_tar = "~{genome_name}.bowtie2.tar"
+  }
+
+  runtime {
+      docker: docker
+      cpu: cpu
+      memory: "~{cpu*2}GiB"
+  }
+}
+
+task hisat2_build {
+  input {
+    Array[File] fasta_gz
+    File? transcripts_gtf_gz
+    String genome_name
+
+    Int cpu = 32
+    String docker
+  }
+
+  command <<<
+    set -euxo pipefail
+    TMPDIR=${TMPDIR:-/tmp}
+
+    all_fasta="$TMPDIR/all.fasta"
+    pigz -dc ~{sep(' ',fasta_gz)} > "$all_fasta"
+
+    mkdir -p "$TMPDIR"'/hisat2/~{genome_name}'
+    if [[ -n '~{transcripts_gtf_gz}' ]]; then
+      # convert GTF per http://daehwankimlab.github.io/hisat2/howto/
+      /hisat2/hisat2_extract_splice_sites.py <(pigz -dc '~{transcripts_gtf_gz}') > "$TMPDIR/genome.ss" & pid=$!
+      /hisat2/hisat2_extract_exons.py <(pigz -dc '~{transcripts_gtf_gz}') > "$TMPDIR/genome.exon"
+      wait $pid
+      >&2 /hisat2/hisat2-build -p 16 \
+        --exon "$TMPDIR/genome.exon" --ss "$TMPDIR/genome.ss" \
+        "$all_fasta" "$TMPDIR"'/hisat2/~{genome_name}/~{genome_name}'
+    else
+      >&2 /hisat2/hisat2-build -p 16 "$all_fasta" "$TMPDIR"'/hisat2/~{genome_name}/~{genome_name}'
+    fi
+    >&2 ls -lR "$TMPDIR/hisat2"
+    env -C "$TMPDIR/hisat2" tar c . > '~{genome_name}.hisat2.tar'
+  >>>
+
+  output {
+    File index_tar = "~{genome_name}.hisat2.tar"
+  }
+
+  runtime {
+    docker: docker
+    cpu: cpu
+    memory: "240G"
+  }
+}
+
+task kallisto_index {
+  input {
+    Array[File] transcripts_fasta_gz
+    String genome_name
+
+    String docker
+  }
+
+  String idx_fn = "~{genome_name}.kallisto.idx"
+  command <<<
+    set -euxo pipefail
+    /kallisto/kallisto index --index '~{idx_fn}' ~{sep(' ',transcripts_fasta_gz)}
+    >&2 ls -l
+  >>>
+
+  output {
+    File idx = idx_fn
+  }
+
+  runtime {
+    docker: docker
+    memory: "16GiB"
+  }
+}
+
+task minimap2_index {
+  input {
+    Array[File] fasta_gz
+    String genome_name
+    String nucleotide_type
+
+    String docker
+  }
+
+  command <<<
+    set -euxo pipefail
+    TMPDIR=${TMPDIR:-/tmp}
+
+    all_fasta="$TMPDIR/all.fasta"
+    pigz -dc ~{sep(' ',fasta_gz)} > "$all_fasta"
+
+    if [ "~{nucleotide_type}" == "dna" ]; then
+        >&2 minimap2 -x map-ont -d '~{genome_name}_{nucleotide_type}.mmi' "$all_fasta"
+    else
+        >&2 minimap2 -x splice -d '~{genome_name}_{nucleotide_type}.mmi' "$all_fasta"
+    fi
+    >&2 ls -l
+  >>>
+
+  output {
+      File index_mmi = "~{genome_name}_{nucleotide_type}.mmi"
+  }
+
+  runtime {
+      docker: docker
+      memory: "32GiB"
+  }
 }
 
-task GenerateHostGenome {
-    input {
-        File input_fasta
-        File? input_gtf
-        String host_name
-        File ercc_fasta
-        File ercc_gtf
-        String docker_image_id
-    }
-
-    command <<<
-        set -euxo pipefail
-
-        #
-        # Create fasta_with_ercc
-        #
-
-        INPUT_FASTA_PATH="~{input_fasta}"
-
-        # Download input fa
-        if [ ${INPUT_FASTA_PATH: -3} == ".gz" ]
-        then
-            gunzip -c $INPUT_FASTA_PATH > input.fa
-            INPUT_FASTA_PATH=input.fa
-        else
-            cp $INPUT_FASTA_PATH input.fa
-            INPUT_FASTA_PATH=input.fa
-        fi
-
-        # Concatenate ercc and input
-        cat "~{ercc_fasta}" $INPUT_FASTA_PATH > fasta_with_ercc.fa
-
-        #
-        # Create gtf_with_ercc
-        #
-
-        INPUT_GTF_PATH="~{input_gtf}"
-        GTF_PATH="~{ercc_gtf}"
-
-        # Download input gtf, if provided
-        if [[ -n "${INPUT_GTF_PATH}" ]] ; then
-            if [ ${INPUT_GTF_PATH: -3} == ".gz" ]
-            then
-                gunzip -c $INPUT_GTF_PATH > input.gtf
-                INPUT_GTF_PATH=input.gtf
-            else
-                cp $INPUT_GTF_PATH input.gtf
-                INPUT_GTF_PATH=input.gtf
-            fi
-            # Concatenate ercc and input
-            cat "~{ercc_gtf}" $INPUT_GTF_PATH > gtf_with_ercc.gtf
-            GTF_PATH=gtf_with_ercc.gtf
-        fi
-
-        #
-        # Generate STAR genome
-        #
-
-        # Make directory for STAR genome
-        STAR_GENOME="~{host_name}_STAR_genome"
-        # HACK: we used to support splitting star indexes into many parts, this made things slower
-        # Here we generate the index as if it is in many parts, but there is only ever one part for
-        # backwards compatibility
-        mkdir -p "$STAR_GENOME/part-0"
-
-        AVAILABLE_MEMORY=$(free --bytes | head -n 2 | tail -n 1 | sed "s/  */ /g" | cut -d' ' -f 7)
-
-        STAR \
-          --sjdbGTFfile $GTF_PATH \
-          --runThreadN $(nproc) \
-          --runMode genomeGenerate \
-          --genomeFastaFiles fasta_with_ercc.fa \
-          --limitGenomeGenerateRAM $AVAILABLE_MEMORY \
-          --genomeDir "$STAR_GENOME/part-0"
-
-        # create a parts.txt file for backwards compatibility
-        echo 1 > "$STAR_GENOME/parts.txt"
-
-        # tar STAR genome
-        tar cvf "$STAR_GENOME.tar" -C $(pwd) $STAR_GENOME
-
-        #
-        # Generate bowtie2 genome
-        #
-
-        # Make directory for bowtie2 genome
-        BOWTIE2_GENOME="~{host_name}_bowtie2_genome"
-        mkdir $BOWTIE2_GENOME
-
-        # Change into the directory to contain the output and generate bowtie2 genome
-        cd $BOWTIE2_GENOME
-        bowtie2-build ../fasta_with_ercc.fa "~{host_name}"
-        cd ..
-
-        # tar bowtie2 genome
-        tar cvf "$BOWTIE2_GENOME.tar" -C $(pwd) $BOWTIE2_GENOME
-
-        minimap2 -x map-ont -d "~{host_name}_minimap2_genome_dna.mmi" fasta_with_ercc.fa
-        minimap2 -x splice -d "~{host_name}_minimap2_genome_rna.mmi" fasta_with_ercc.fa
-    >>>
-
-    output {
-        File original_input_fasta = "input.fa"
-        File? original_input_gtf = "input.gtf"
-        File fasta_with_ercc_fa = "fasta_with_ercc.fa"
-        File? gtf_with_ercc_gtf = "gtf_with_ercc.gtf"
-        File star_genome_tar = "~{host_name}_STAR_genome.tar"
-        File bowtie_genome_tar = "~{host_name}_bowtie2_genome.tar"
-        File minimap2_dna = "~{host_name}_minimap2_genome_dna.mmi"
-        File minimap2_rna = "~{host_name}_minimap2_genome_rna.mmi"
-    }
-
-    runtime {
-        docker: docker_image_id
-    }
+task star_generate {
+  input {
+    Array[File] fasta_gz
+    File? transcripts_gtf_gz
+    String genome_name
+
+
+    Int cpu = 32
+    String docker
+  }
+
+  command <<<
+    set -euxo pipefail
+    TMPDIR=${TMPDIR:-/tmp}
+
+    all_fasta="$TMPDIR/all.fasta"
+    pigz -dc ~{sep(' ',fasta_gz)} > "$all_fasta"
+
+    gtf_flag=""
+    if [[ -n '~{transcripts_gtf_gz}' ]]; then
+      transcripts_gtf="$TMPDIR/transcripts.gtf"
+      pigz -dc '~{transcripts_gtf_gz}' > "$transcripts_gtf"
+      gtf_flag = "--sjdbGTFfile \"$transcripts_gtf\""
+    fi
+
+    # Make directory for STAR genome
+    STAR_GENOME="~{genome_name}_STAR_genome"
+    # HACK: we used to support splitting star indexes into many parts, this made things slower
+    # Here we generate the index as if it is in many parts, but there is only ever one part for
+    # backwards compatibility
+    mkdir -p "$STAR_GENOME/part-0"
+
+    STAR \
+      --sjdbGTFfile "~{transcripts_gtf_gz}" \
+      --runThreadN ~{cpu} \
+      --runMode genomeGenerate \
+      --genomeFastaFiles "$all_fasta" \
+      --limitGenomeGenerateRAM 64000000000 \
+      --genomeDir "$STAR_GENOME/part-0" $gtf_flag
+
+    # create a parts.txt file for backwards compatibility
+    echo 1 > "$STAR_GENOME/parts.txt"
+
+    # tar STAR genome
+    tar cvf "$STAR_GENOME.tar" -C $(pwd) $STAR_GENOME
+  >>>
+
+  output {
+      File star_genome_tar = "~{genome_name}_STAR_genome.tar"
+  }
+
+  runtime {
+      docker: docker
+      cpu: cpu
+      memory: "64GiB"
+  }
 }
diff --git a/workflows/host-genome-generation/test/test_wdl.py b/workflows/host-genome-generation/test/test_wdl.py
index 666e1ff93..8fe9ac77b 100644
--- a/workflows/host-genome-generation/test/test_wdl.py
+++ b/workflows/host-genome-generation/test/test_wdl.py
@@ -7,10 +7,9 @@ class TestIndexGeneration(WDLTestCase):
 
     wdl = os.path.join(os.path.dirname(__file__), "..", "host_genome_generation.wdl")
     common_inputs = {
-        "input_fasta": os.path.join(os.path.dirname(__file__), "fixtures/input.fasta"),
-        "host_name": "test",
-        "ercc_fasta": os.path.join(os.path.dirname(__file__), "fixtures/ERCC.fasta"),
-        "ercc_gtf": os.path.join(os.path.dirname(__file__), "fixtures/ERCC.gtf"),
+        "genome_name": "test",
+        "genome_fasta_gz": os.path.join(os.path.dirname(__file__), "fixtures/input.fasta"),
+        "ERCC_fasta_gz": os.path.join(os.path.dirname(__file__), "fixtures/ERCC.fasta"),
     }
 
     def testIndexGeneration(self):

From 86a0a38acee68f1815919d870ba1f658d04115bb Mon Sep 17 00:00:00 2001
From: morsecodist <todd@morsecodist.io>
Date: Thu, 2 Feb 2023 09:47:41 -0800
Subject: [PATCH 02/13] add concat unzip step + docker_image_id

---
 .../host_genome_generation.wdl                | 117 +++++++++++-------
 1 file changed, 70 insertions(+), 47 deletions(-)

diff --git a/workflows/host-genome-generation/host_genome_generation.wdl b/workflows/host-genome-generation/host_genome_generation.wdl
index f29be4395..e6d08ac08 100644
--- a/workflows/host-genome-generation/host_genome_generation.wdl
+++ b/workflows/host-genome-generation/host_genome_generation.wdl
@@ -28,7 +28,7 @@ workflow host_filter_indexing {
     # Sequence names must be unique among all FASTAs!
     Array[File] other_fasta_gz = []
 
-    String docker
+    String docker_image_id
   }
 
   call ensure_gz as genome_fasta {
@@ -36,45 +36,59 @@ workflow host_filter_indexing {
     # existing host genome FASTAs which we archived without compression.
     input:
     maybe_gz = genome_fasta_gz,
-    docker
+    docker_image_id
   }
 
-  call bowtie2_build {
+  call concatenate_and_unzip_fastas {
     input:
     fasta_gz = flatten([[genome_fasta.gz, ERCC_fasta_gz], other_fasta_gz]),
-    genome_name, docker
+    docker_image_id,
+  }
+
+  call bowtie2_build {
+    input:
+    fasta = concatenate_and_unzip_fastas.fasta,
+    genome_name,
+    docker_image_id,
   }
 
   call hisat2_build {
     input:
-    fasta_gz = flatten([[genome_fasta.gz, ERCC_fasta_gz], other_fasta_gz]),
-    transcripts_gtf_gz, genome_name, docker
+    fasta = concatenate_and_unzip_fastas.fasta,
+    transcripts_gtf_gz,
+    genome_name,
+    docker_image_id,
   }
 
   call kallisto_index {
     input:
     transcripts_fasta_gz = flatten([transcripts_fasta_gz, [ERCC_fasta_gz]]),
-    genome_name, docker
+    genome_name,
+    docker_image_id,
   }
 
   call minimap2_index as minimap2_index_dna {
     input:
-    fasta_gz = flatten([[genome_fasta.gz, ERCC_fasta_gz], other_fasta_gz]),
+    fasta = concatenate_and_unzip_fastas.fasta,
     nucleotide_type = "dna",
-    genome_name, docker
+    genome_name,
+    docker_image_id,
   }
 
   call minimap2_index as minimap2_index_rna {
     input:
-    fasta_gz = flatten([[genome_fasta.gz, ERCC_fasta_gz], other_fasta_gz]),
+    fasta = concatenate_and_unzip_fastas.fasta,
     nucleotide_type = "rna",
-    genome_name, docker
+    genome_name,
+    docker_image_id,
   }
 
   call star_generate {
     input:
-    fasta_gz = flatten([[genome_fasta.gz, ERCC_fasta_gz], other_fasta_gz]),
-    transcripts_gtf_gz, genome_name, docker
+    fasta = concatenate_and_unzip_fastas.fasta,
+    transcripts_gtf_gz,
+    genome_name,
+    docker_image_id,
   }
 
   output {
@@ -97,7 +111,7 @@ workflow host_filter_indexing {
 task ensure_gz {
   input {
     File maybe_gz
-    String docker
+    String docker_image_id
   }
 
   String name = basename(maybe_gz)
@@ -117,31 +131,49 @@ task ensure_gz {
   }
 
   runtime {
-      docker: docker
+      docker: docker_image_id
       cpu: 4
       memory: "4GiB"
   }
 }
 
-task bowtie2_build {
+task concatenate_and_unzip_fastas {
   input {
     Array[File] fasta_gz
+    String docker_image_id
+  }
+
+  command <<<
+    pigz -dc ~{sep(' ',fasta_gz)} > "all.fasta"
+  >>>
+
+  output {
+      File fasta = "all.fasta"
+  }
+
+  runtime {
+      docker: docker_image_id
+      cpu: 4
+      memory: "4GiB"
+  }
+}
+
+task bowtie2_build {
+  input {
+    File fasta
     String genome_name
     Int seed = 42
 
     Int cpu = 16
-    String docker
+    String docker_image_id
   }
 
   command <<<
     set -euxo pipefail
     TMPDIR=${TMPDIR:-/tmp}
 
-    all_fasta="$TMPDIR/all.fasta"
-    pigz -dc ~{sep(' ',fasta_gz)} > "$all_fasta"
-
     mkdir -p "$TMPDIR"'/bt2/~{genome_name}'
-    >&2 bowtie2-build --seed ~{seed} --threads ~{cpu} "$all_fasta" "$TMPDIR"'/bt2/~{genome_name}/~{genome_name}'
+    >&2 bowtie2-build --seed ~{seed} --threads ~{cpu} "~{fasta}" "$TMPDIR"'/bt2/~{genome_name}/~{genome_name}'
     >&2 ls -lR "$TMPDIR/bt2"
     env -C "$TMPDIR/bt2" tar c . > '~{genome_name}.bowtie2.tar'
   >>>
@@ -151,7 +183,7 @@ task bowtie2_build {
   }
 
   runtime {
-      docker: docker
+      docker: docker_image_id
       cpu: cpu
       memory: "~{cpu*2}GiB"
   }
@@ -159,21 +191,18 @@ task bowtie2_build {
 
 task hisat2_build {
   input {
-    Array[File] fasta_gz
+    File fasta
     File? transcripts_gtf_gz
     String genome_name
 
     Int cpu = 32
-    String docker
+    String docker_image_id
   }
 
   command <<<
     set -euxo pipefail
     TMPDIR=${TMPDIR:-/tmp}
 
-    all_fasta="$TMPDIR/all.fasta"
-    pigz -dc ~{sep(' ',fasta_gz)} > "$all_fasta"
-
     mkdir -p "$TMPDIR"'/hisat2/~{genome_name}'
     if [[ -n '~{transcripts_gtf_gz}' ]]; then
       # convert GTF per http://daehwankimlab.github.io/hisat2/howto/
@@ -182,9 +211,9 @@ task hisat2_build {
       wait $pid
       >&2 /hisat2/hisat2-build -p 16 \
         --exon "$TMPDIR/genome.exon" --ss "$TMPDIR/genome.ss" \
-        "$all_fasta" "$TMPDIR"'/hisat2/~{genome_name}/~{genome_name}'
+        "~{fasta}" "$TMPDIR"'/hisat2/~{genome_name}/~{genome_name}'
     else
-      >&2 /hisat2/hisat2-build -p 16 "$all_fasta" "$TMPDIR"'/hisat2/~{genome_name}/~{genome_name}'
+      >&2 /hisat2/hisat2-build -p 16 "~{fasta}" "$TMPDIR"'/hisat2/~{genome_name}/~{genome_name}'
     fi
     >&2 ls -lR "$TMPDIR/hisat2"
     env -C "$TMPDIR/hisat2" tar c . > '~{genome_name}.hisat2.tar'
@@ -195,7 +224,7 @@ task hisat2_build {
   }
 
   runtime {
-    docker: docker
+    docker: docker_image_id
     cpu: cpu
     memory: "240G"
   }
@@ -206,7 +235,7 @@ task kallisto_index {
     Array[File] transcripts_fasta_gz
     String genome_name
 
-    String docker
+    String docker_image_id
   }
 
   String idx_fn = "~{genome_name}.kallisto.idx"
@@ -221,31 +250,28 @@ task kallisto_index {
   }
 
   runtime {
-    docker: docker
+    docker: docker_image_id
     memory: "16GiB"
   }
 }
 
 task minimap2_index {
   input {
-    Array[File] fasta_gz
+    File fasta
     String genome_name
     String nucleotide_type
 
-    String docker
+    String docker_image_id
   }
 
   command <<<
     set -euxo pipefail
     TMPDIR=${TMPDIR:-/tmp}
 
-    all_fasta="$TMPDIR/all.fasta"
-    pigz -dc ~{sep(' ',fasta_gz)} > "$all_fasta"
-
     if [ "~{nucleotide_type}" == "dna" ]; then
-        >&2 minimap2 -x map-ont -d '~{genome_name}_{nucleotide_type}.mmi' "$all_fasta"
+        >&2 minimap2 -x map-ont -d '~{genome_name}_{nucleotide_type}.mmi' "~{fasta}"
     else
-        >&2 minimap2 -x splice -d '~{genome_name}_{nucleotide_type}.mmi' "$all_fasta"
+        >&2 minimap2 -x splice -d '~{genome_name}_{nucleotide_type}.mmi' "~{fasta}"
     fi
     >&2 ls -l
   >>>
@@ -255,29 +281,26 @@ task minimap2_index {
   }
 
   runtime {
-      docker: docker
+      docker: docker_image_id
       memory: "32GiB"
   }
 }
 
 task star_generate {
   input {
-    Array[File] fasta_gz
+    File fasta
     File? transcripts_gtf_gz
     String genome_name
 
 
     Int cpu = 32
-    String docker
+    String docker_image_id
   }
 
   command <<<
     set -euxo pipefail
     TMPDIR=${TMPDIR:-/tmp}
 
-    all_fasta="$TMPDIR/all.fasta"
-    pigz -dc ~{sep(' ',fasta_gz)} > "$all_fasta"
-
     gtf_flag=""
     if [[ -n '~{transcripts_gtf_gz}' ]]; then
       transcripts_gtf="$TMPDIR/transcripts.gtf"
@@ -296,7 +319,7 @@ task star_generate {
       --sjdbGTFfile "~{transcripts_gtf_gz}" \
       --runThreadN ~{cpu} \
       --runMode genomeGenerate \
-      --genomeFastaFiles "$all_fasta" \
+      --genomeFastaFiles "~{fasta}" \
       --limitGenomeGenerateRAM 64000000000 \
       --genomeDir "$STAR_GENOME/part-0" $gtf_flag
 
@@ -312,7 +335,7 @@ task star_generate {
   }
 
   runtime {
-      docker: docker
+      docker: docker_image_id
       cpu: cpu
       memory: "64GiB"
   }

From 03eade9557b6ee58429cd96945a70ee9e8a14522 Mon Sep 17 00:00:00 2001
From: morsecodist <todd@morsecodist.io>
Date: Thu, 2 Feb 2023 09:56:40 -0800
Subject: [PATCH 03/13] update docker

---
 workflows/host-genome-generation/Dockerfile | 25 +++++++++++++++++++--
 1 file changed, 23 insertions(+), 2 deletions(-)

diff --git a/workflows/host-genome-generation/Dockerfile b/workflows/host-genome-generation/Dockerfile
index 63ff42161..c979eb516 100644
--- a/workflows/host-genome-generation/Dockerfile
+++ b/workflows/host-genome-generation/Dockerfile
@@ -2,10 +2,31 @@
 FROM ubuntu:22.04
 ARG DEBIAN_FRONTEND=noninteractive
 
-# this brings in python2.7
-RUN apt-get update && apt-get install -y bowtie2 curl minimap2
+# This brings in python2.7
+RUN apt-get update && apt-get install -y bowtie2 curl minimap2 pigz dh-autoreconf nasm
 
 # Install STAR, the package rna-star does not include STARlong
 RUN curl -L https://github.com/alexdobin/STAR/archive/2.5.3a.tar.gz | tar xz
 RUN mv STAR-2.5.3a/bin/Linux_x86_64_static/* /usr/local/bin
 RUN rm -rf STAR-2.5.3a
+
+# Install fastp (libdeflate libisal (dh-autoreconf nasm))
+WORKDIR /tmp
+RUN wget -nv -O - https://github.com/intel/isa-l/archive/refs/tags/v2.30.0.tar.gz | tar zx
+RUN cd isa-l-* && ./autogen.sh && ./configure && make -j8 && make install
+RUN wget -nv -O - https://github.com/ebiggers/libdeflate/archive/refs/tags/v1.12.tar.gz | tar zx
+RUN cd libdeflate-* && make -j8 && make install
+RUN ldconfig
+RUN git clone https://github.com/mlin/fastp.git && git -C fastp checkout 37edd60
+RUN cd fastp && make -j8 && ./fastp test && cp fastp /usr/local/bin
+
+# Install hisat2
+WORKDIR /hisat2
+RUN wget -nv -O /tmp/HISAT2.zip https://cloud.biohpc.swmed.edu/index.php/s/oTtGWbWjaxsQ2Ho/download \
+    && unzip /tmp/HISAT2.zip && mv hisat2-*/* . && rm /tmp/HISAT2.zip
+
+# Install kallisto + python gtfparse
+RUN curl -L https://github.com/pachterlab/kallisto/releases/download/v0.46.1/kallisto_linux-v0.46.1.tar.gz | tar xz -C /
+RUN pip3 install gtfparse==1.2.1
+
+WORKDIR /
\ No newline at end of file

From 558ff43c1448e2a9a1b1d747687a7409ddeb0352 Mon Sep 17 00:00:00 2001
From: morsecodist <todd@morsecodist.io>
Date: Thu, 2 Feb 2023 11:52:34 -0800
Subject: [PATCH 04/13] install docker dependencies

---
 workflows/host-genome-generation/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/host-genome-generation/Dockerfile b/workflows/host-genome-generation/Dockerfile
index c979eb516..d49538a1e 100644
--- a/workflows/host-genome-generation/Dockerfile
+++ b/workflows/host-genome-generation/Dockerfile
@@ -3,7 +3,7 @@ FROM ubuntu:22.04
 ARG DEBIAN_FRONTEND=noninteractive
 
 # This brings in python2.7
-RUN apt-get update && apt-get install -y bowtie2 curl minimap2 pigz dh-autoreconf nasm
+RUN apt-get update && apt-get install -y wget bowtie2 curl minimap2 pigz dh-autoreconf nasm make git g++ unzip python3-pip
 
 # Install STAR, the package rna-star does not include STARlong
 RUN curl -L https://github.com/alexdobin/STAR/archive/2.5.3a.tar.gz | tar xz

From 4556f51bb431ddc8e31f07a3fb7a42b852150848 Mon Sep 17 00:00:00 2001
From: morsecodist <todd@morsecodist.io>
Date: Thu, 2 Feb 2023 13:14:50 -0800
Subject: [PATCH 05/13] gzip inputs

---
 .../test/fixtures/ERCC.fasta                  |  87 ---------------
 .../test/fixtures/ERCC.fasta.gz               | Bin 0 -> 1688 bytes
 .../test/fixtures/ERCC.gtf                    |  92 ----------------
 .../test/fixtures/input.fasta                 | 100 ------------------
 .../test/fixtures/input.fasta.gz              | Bin 0 -> 2637 bytes
 .../host-genome-generation/test/test_wdl.py   |   4 +-
 6 files changed, 2 insertions(+), 281 deletions(-)
 delete mode 100644 workflows/host-genome-generation/test/fixtures/ERCC.fasta
 create mode 100644 workflows/host-genome-generation/test/fixtures/ERCC.fasta.gz
 delete mode 100644 workflows/host-genome-generation/test/fixtures/ERCC.gtf
 delete mode 100644 workflows/host-genome-generation/test/fixtures/input.fasta
 create mode 100644 workflows/host-genome-generation/test/fixtures/input.fasta.gz

diff --git a/workflows/host-genome-generation/test/fixtures/ERCC.fasta b/workflows/host-genome-generation/test/fixtures/ERCC.fasta
deleted file mode 100644
index e23afdb39..000000000
--- a/workflows/host-genome-generation/test/fixtures/ERCC.fasta
+++ /dev/null
@@ -1,87 +0,0 @@
->ERCC-00002
-TCCAGATTACTTCCATTTCCGCCCAAGCTGCTCACAGTATACGGGCGTCGGCATCCAGAC
-CGTCGGCTGATCGTGGTTTTACTAGGCTAGACTAGCGTACGAGCACTATGGTCAGTAATT
-CCTGGAGGAATAGGTACCAAGAAAAAAACGAACCTTTGGGTTCCAGAGCTGTACGGTCGC
-ACTGAACTCGGATAGGTCTCAGAAAAACGAAATATAGGCTTACGGTAGGTCCGAATGGCA
-CAAAGCTTGTTCCGTTAGCTGGCATAAGATTCCATGCCTAGATGTGATACACGTTTCTGG
-AAACTGCCTCGTCATGCGACTGTTCCCCGGGGTCAGGGCCGCTGGTATTTGCTGTAAAGA
-GGGGCGTTGAGTCCGTCCGACTTCACTGCCCCCTTTCAGCCTTTTGGGTCCTGTATCCCA
-ATTCTCAGAGGTCCCGCCGTACGCTGAGGACCACCTGAAACGGGCATCGTCGCTCTTCGT
-TGTTCGTCGACTTCTAGTGTGGAGACGAATTGCCAGAATTATTAACTGCGCAGTTAGGGC
-AGCGTCTGAGGAAGTTTGCTGCGGTTTCGCCTTGACCGCGGGAAGGAGACATAACGATAG
-CGACTCTGTCTCAGGGGATCTGCATATGTTTGCAGCATACTTTAGGTGGGCCTTGGCTTC
-CTTCCGCAGTCAAAACCGCGCAATTATCCCCGTCCTGATTTACTGGACTCGCAACGTGGG
-TCCATCAGTTGTCCGTATACCAAGACGTCTAAGGGCGGTGTACACCCTTTTGAGCAATGA
-TTGCACAACCTGCGATCACCTTATACAGAATTATCAATCAAGCTCCCCGAGGAGCGGACT
-TGTAAGGACCGCCGCTTTCGCTCGGGTCTGCGGGTTATAGCTTTTCAGTCTCGACGGGCT
-AGCACACATCTGGTTGACTAGGCGCATAGTCGCCATTCACAGATTTGCTCGGCAATCAGT
-ACTGGTAGGCGTTAGACCCCGTGACTCGTGGCTGAACGGCCGTACAACTCGACAGCCGGT
-GCTTGCGTTTTACCCTTAAAAAAAAAAAAAAAAAAAAAAAA
->ERCC-00003
-CAGCAGCGATTAAGGCAGAGGCGTTTGTATCTGCCATTATAAAGAAGTTTCCTCCAGCAA
-CTCCTTTCTTAATTCCAAACTTAGCTTCAGTTATAAATTCCCCTCCCATGATTGGGATTT
-TATAAACTTTTCTTCCATATAATTCATCTTTCTTCTCATAACCGTCTCCGAAAAACTTCA
-ACTTAAATCCAACCTTTAACTGCTCATCAGCCATGTCTCCCACAGCATCAAAAATAGCAG
-TTGTTGGACATGTTAAGACACACTGCCCCAATCTCTCTAACATTTGATGCTCTAACTCTG
-ACTTTTTAGGGTGGCATATCTGTATTATAAATCCTGGTCTTCCATCTGGTGTTTTTGATG
-GAGGGACATATTTCTCAATTCCTGCTTCTGCTGGACACATTATAACTGAACAACCAAAAC
-CTGTTGCCTCTGTAGCTGCAATCTTAGCCCACTTCTTTGTAGCTGCTGTTATTAAAACTC
-TTGAAACCCATATTGGGAATGCTTCTGCAAATGTATCTTCAATATATACTCCATTTATTT
-CCATAGTTTCCCTCCATTAAGATTTTAACAATTATAGTTTATCTTAGGGGCTATTAATAT
-CTTATCATTTGGTTTTTAATATTCGATAAATCCATAAATAAAAATATATCAACAATAATT
-TTAAATAATCTAAGTATAGGTAATATAACAATTAAAAAGATTTAGAGGGATAGAATTGAA
-CGGCATTAGGAGAATTGTTTTAGATATATTGAAGCCGCATGAGCCAAAAATAACAGATAT
-GGCATTAAAATTAACATCATTATCAAACATTGATGGGGTTAATATTACAGTCTATGAAAT
-AGATAAAGAGACTGAGAATGTTAAAGTTACAATTGAAGGGAATAATTTAGATTTTGATGA
-GATTCAGGAAATTATTGAAAGTTTGGGAGGGACTATTCACAGTATAGATGAGGTTGTTGC
-AGGTAAAAAGATTATTGAAGAGTTAGAACACCACAAGATAAAAAAAAAAAAAAAAAAAAA
-AAA
->ERCC-00004
-TCTTGCTTCAACAATAACGTCTCTTTCAGAAGGCATTGGTATCTTTTCCCCACTTCCAAG
-CATTTTTTCAACTAATCTTATGTTATTAACCATTTCCTTAAATTCTTCTGGGTCTGCTGA
-CAAAGCATGATCAGGACCTTCCATATTTTTATYTAAGGTAAAGTGCTTCTCAATAACATC
-CGCTCCTAAGGCAACAGAAACTACTGGGGCGAGTATTCCCAATGTATGGTCAGAATATCC
-CACAGGGATATTGAATATACTTTTCAAGGTTTTAATAGCGTTTAAATTGACATCTTCATA
-AGGGGTTGGGTAAGATGAAATACAATGCAATAAAATAATATCCCTGCATCCATTATTTTC
-TAAAACTTTAACTGCTTCCCAAATTTCCCCAATATCAGACATTCCTGTAGATAAAATCAC
-CGGCTTGCCTGTTTTTGCCACTTTTTCTAATAAGGGATAAAAGGTTAAATCACCAGAGGC
-AATTTTAAATCAGGCACATAAAAAAAAAAAAAAAAAAAAAAAA
->ERCC-00007
-TTTATTGGTACGTAATTTCGTCAACCGTTTTTCGGTCTAACTTCTTAATGACTTCTGTAA
-TTAACTTTACCGCGTTTTCATAATCATCACGATGCAGCATGGCCGCGTGCGTATGAATGT
-AGCGGGTTGCAATGGTAATGGACAGCGCAGGAACGCCATTTGCCGTCAAATGGATGGCAC
-CCGAATCAGTTCCGCCGCCGGCAATGGCATCAAATTGGTACGGAATGCCGGCTTCCTCCG
-CAGTGGCTACAACTGCATCGCGCAAACCTTTGTGAGAGACCATGGATGCATCGTAAACGA
-TAATCTGCGGGCCTTTGCCCATTTTGCTCTGCGCTTCCTTCTCGGAAATGCCAGGCGTGT
-CTCCTGCTATCCCTACATCAACACCAAACGCAATATCAGGCTGAATGGTGTGTGCAGCCG
-TTTTCGCTCCCCTCAGCCCGACTTCCTCCTGCACGGTTCCGACGCCATACACTATATTTG
-GATGATCTGTGTTTTGTAAGTTTCTTAACACATCAATAGCAATCGCACAGCCGATGCGGT
-TGTCCCAGGCCTTTGCGAGTAGGAATTTTTCATTGTTCATGACCGTAAATTCAAAATGCG
-GAACGATCATATCTCCCGGAAGTACACCCCACTCCAAGGCTTCTTCCCGGCTTGAAGCTC
-CAATATCAATAAACATGTCTTTTATTTCCACTGATTTTTTTCTTGCTTCAGGAGACAAAA
-TATGAGGCGGCTTAGATCCGATAACCCCTGTGATTTCTCCTTTTTTTGTGACAATGGTGA
-CGCGCTGAGCAAGCATAACCTGAGCCCACCAGCCGCCAACGGTTTGAAAACGGATAAAGC
-CTTTATCTGTGATTTGTGTCACCATAAAGCCGACTTCATCCAAATGTCCGGCGATCATAA
-TTTTCGGGCCGTTTTCTGCACCAGTTTTTTTTGCAATTAAACTGCCCAGGCGATCTGTTG
-TCACCTCATCAGCAAATGGTTCTATGTATGATTTCATCACTTGCCTTACTTCTCTTTCAT
-TGCCCGGTATGCCTTTTGCATCTGTTAAATCTTTCAGCATGGTCAATGTTTCATCTAATT
-TTGCCATGTTCCAAACCCTCCTTGAGCTCGGAAAAAAAAAAAAAAAAAAAAAAAA
->ERCC-00009
-CAATGATAGGCTAGTCTCGCGCAGTACATGGTAGTTCAGCCAATAGATGCCTAGTACGCT
-GACGGCATTCAGAGTACGCTGATCGGCTTATGACGTATGTGACGCAGCTCTTAGCGCAAT
-GTATGTGCTGTTATCGAAGCCTATGGCTGAGTATGTAACGCTATGGCGTGCTAGTCGTCT
-CATATACGTCTGATGACCTCGTATCATGTTATAGGGCTGCGAACTGTCGATGATGGTCAC
-GACTCTGTCGATAGCTGTGTGACTCATTCAGAAGGTGTGCAGCCTATATGATACGCAGTC
-GCATCCTATCTTACGTGTCAGTACTATGTGTGAGTGCTCCGCCCTAGTGCTGATGTATGC
-CCCATAGTGCTCAGTGGAGTCTCTCTTAGCATAGTGTCCGCTCATACATTAGATGGACGG
-CTCATTAGTATCATCGTCGGCTGATATAGGTCGTGGCTCCCTGTATATCGAGGTGAGTCT
-ATCTGGATCAACGTCGCACTATGATGTGCAAAGTGTCGTCCATGTATAGACAGTGCGCGT
-ATCATATAGGATGCGGCGATCTCATACAGCGTTACGGTCGCTGCGTACTGTATAAGGATG
-CTCTGTGAACTGTCATCGGTCCGATCAATTAGTCTAGTGTGCGTTATTCAGATCGAGTGA
-GTACATGATTCGTCAGTGTGGATCAATTACAGTTAGGCCGCTGACACATTAGTAACGTCG
-GCAAGCACTTAGTCGTGTCGTAAGCCAGTGTGTCGTGTCTTAGACGACTGTGTGTGATTC
-TCGAGCGATTTATACATCCGTGACAGCGCTTATAGTGTGCTGACAGACTGGTTGGTTATC
-CAATGATCGACCTGGAGTCTAATATCTGACCACGCCTTGTAATCGTATGACACGCGCTTG
-ACACGACTGAATCCAGCTTAAGAGCCCTGCAACGCGATATACAGGCGCTGCTACCGATAT
-AAAAAAAAAAAAAAAAAAAAAAAA
-
diff --git a/workflows/host-genome-generation/test/fixtures/ERCC.fasta.gz b/workflows/host-genome-generation/test/fixtures/ERCC.fasta.gz
new file mode 100644
index 0000000000000000000000000000000000000000..a2dcf25384d2d2c7b615360e529f47046e40cf4f
GIT binary patch
literal 1688
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zSXnD|TEWZhZcd-QcU9&8%a{G_&%ZK%`uYC+aym0Ax+8nO_Iy^}Z&BIzFXKM%xX-I9
ztM9+NicNX;y6*w^Yt`L72gTf*1^46LzgzGBxtb*$cjcVC`|g9f7x(k78kynG-Ept)
zX*Gu;ZN#9(6_qDO=>53YZXZqSvo|`_!W}G_`#sv9D`<{uj=mq9J!S>27&lxOj0Jbe
zoPU)c+h)}n2|OO-XW`h%NjWaUz<XG7W{*SFe9k_l6YrrYgi_;pk4#Ly`}vRU$=*3U
z&Zvf!+@C1nknzOz!d;O##Yhp6c{s;cA5@$>$h)?UX*EF_w~X}Q%lx5DO`sZE4q;q5
za~G46cqht^__;BUIdpuPgytY}%t&1`$<lbcJu0{ulgBcgH^z^iC(Xxk7qLwgLr)xz
zgTk~c1kGcTvB+)mt@U=iB*U7(wvkAH*XP0UH&kerq~XN4aW6+aN6kX(1XZv+QQ{Er
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literal 0
HcmV?d00001

diff --git a/workflows/host-genome-generation/test/fixtures/ERCC.gtf b/workflows/host-genome-generation/test/fixtures/ERCC.gtf
deleted file mode 100644
index cf2d5921b..000000000
--- a/workflows/host-genome-generation/test/fixtures/ERCC.gtf
+++ /dev/null
@@ -1,92 +0,0 @@
-ERCC-00002	ERCC	exon	1	1061	0.000000	+	.	gene_id "ERCC-00002"; transcript_id "DQ459430";
-ERCC-00003	ERCC	exon	1	1023	0.000000	+	.	gene_id "ERCC-00003"; transcript_id "DQ516784";
-ERCC-00004	ERCC	exon	1	523	0.000000	+	.	gene_id "ERCC-00004"; transcript_id "DQ516752";
-ERCC-00009	ERCC	exon	1	984	0.000000	+	.	gene_id "ERCC-00009"; transcript_id "DQ668364";
-ERCC-00012	ERCC	exon	1	994	0.000000	+	.	gene_id "ERCC-00012"; transcript_id "DQ883670";
-ERCC-00013	ERCC	exon	1	808	0.000000	+	.	gene_id "ERCC-00013"; transcript_id "EF011062";
-ERCC-00014	ERCC	exon	1	1957	0.000000	+	.	gene_id "ERCC-00014"; transcript_id "DQ875385";
-ERCC-00016	ERCC	exon	1	844	0.000000	+	.	gene_id "ERCC-00016"; transcript_id "DQ883664";
-ERCC-00017	ERCC	exon	1	1136	0.000000	+	.	gene_id "ERCC-00017"; transcript_id "DQ459420";
-ERCC-00019	ERCC	exon	1	644	0.000000	+	.	gene_id "ERCC-00019"; transcript_id "DQ883651";
-ERCC-00022	ERCC	exon	1	751	0.000000	+	.	gene_id "ERCC-00022"; transcript_id "DQ855004";
-ERCC-00024	ERCC	exon	1	536	0.000000	+	.	gene_id "ERCC-00024"; transcript_id "DQ854993";
-ERCC-00025	ERCC	exon	1	1994	0.000000	+	.	gene_id "ERCC-00025"; transcript_id "DQ883689";
-ERCC-00028	ERCC	exon	1	1130	0.000000	+	.	gene_id "ERCC-00028"; transcript_id "DQ459419";
-ERCC-00031	ERCC	exon	1	1138	0.000000	+	.	gene_id "ERCC-00031"; transcript_id "DQ459431";
-ERCC-00033	ERCC	exon	1	2022	0.000000	+	.	gene_id "ERCC-00033"; transcript_id "DQ516796";
-ERCC-00034	ERCC	exon	1	1019	0.000000	+	.	gene_id "ERCC-00034"; transcript_id "DQ855001";
-ERCC-00035	ERCC	exon	1	1130	0.000000	+	.	gene_id "ERCC-00035"; transcript_id "DQ459413";
-ERCC-00039	ERCC	exon	1	740	0.000000	+	.	gene_id "ERCC-00039"; transcript_id "DQ883656";
-ERCC-00040	ERCC	exon	1	744	0.000000	+	.	gene_id "ERCC-00040"; transcript_id "DQ883661";
-ERCC-00041	ERCC	exon	1	1122	0.000000	+	.	gene_id "ERCC-00041"; transcript_id "EF011069";
-ERCC-00042	ERCC	exon	1	1023	0.000000	+	.	gene_id "ERCC-00042"; transcript_id "DQ516783";
-ERCC-00043	ERCC	exon	1	1023	0.000000	+	.	gene_id "ERCC-00043"; transcript_id "DQ516787";
-ERCC-00044	ERCC	exon	1	1156	0.000000	+	.	gene_id "ERCC-00044"; transcript_id "DQ459424";
-ERCC-00046	ERCC	exon	1	522	0.000000	+	.	gene_id "ERCC-00046"; transcript_id "DQ516748";
-ERCC-00048	ERCC	exon	1	992	0.000000	+	.	gene_id "ERCC-00048"; transcript_id "DQ883671";
-ERCC-00051	ERCC	exon	1	274	0.000000	+	.	gene_id "ERCC-00051"; transcript_id "DQ516740";
-ERCC-00053	ERCC	exon	1	1023	0.000000	+	.	gene_id "ERCC-00053"; transcript_id "DQ516785";
-ERCC-00054	ERCC	exon	1	274	0.000000	+	.	gene_id "ERCC-00054"; transcript_id "DQ516731";
-ERCC-00057	ERCC	exon	1	1021	0.000000	+	.	gene_id "ERCC-00057"; transcript_id "DQ668366";
-ERCC-00058	ERCC	exon	1	1136	0.000000	+	.	gene_id "ERCC-00058"; transcript_id "DQ459418";
-ERCC-00059	ERCC	exon	1	525	0.000000	+	.	gene_id "ERCC-00059"; transcript_id "DQ668356";
-ERCC-00060	ERCC	exon	1	523	0.000000	+	.	gene_id "ERCC-00060"; transcript_id "DQ516763";
-ERCC-00061	ERCC	exon	1	1136	0.000000	+	.	gene_id "ERCC-00061"; transcript_id "DQ459426";
-ERCC-00062	ERCC	exon	1	1023	0.000000	+	.	gene_id "ERCC-00062"; transcript_id "DQ516786";
-ERCC-00067	ERCC	exon	1	644	0.000000	+	.	gene_id "ERCC-00067"; transcript_id "DQ883653";
-ERCC-00069	ERCC	exon	1	1137	0.000000	+	.	gene_id "ERCC-00069"; transcript_id "DQ459421";
-ERCC-00071	ERCC	exon	1	642	0.000000	+	.	gene_id "ERCC-00071"; transcript_id "DQ883654";
-ERCC-00073	ERCC	exon	1	603	0.000000	+	.	gene_id "ERCC-00073"; transcript_id "DQ668358";
-ERCC-00074	ERCC	exon	1	522	0.000000	+	.	gene_id "ERCC-00074"; transcript_id "DQ516754";
-ERCC-00075	ERCC	exon	1	1023	0.000000	+	.	gene_id "ERCC-00075"; transcript_id "DQ516778";
-ERCC-00076	ERCC	exon	1	642	0.000000	+	.	gene_id "ERCC-00076"; transcript_id "DQ883650";
-ERCC-00077	ERCC	exon	1	273	0.000000	+	.	gene_id "ERCC-00077"; transcript_id "DQ516742";
-ERCC-00078	ERCC	exon	1	993	0.000000	+	.	gene_id "ERCC-00078"; transcript_id "DQ883673";
-ERCC-00079	ERCC	exon	1	644	0.000000	+	.	gene_id "ERCC-00079"; transcript_id "DQ883652";
-ERCC-00081	ERCC	exon	1	534	0.000000	+	.	gene_id "ERCC-00081"; transcript_id "DQ854991";
-ERCC-00083	ERCC	exon	1	1022	0.000000	+	.	gene_id "ERCC-00083"; transcript_id "DQ516780";
-ERCC-00084	ERCC	exon	1	994	0.000000	+	.	gene_id "ERCC-00084"; transcript_id "DQ883682";
-ERCC-00085	ERCC	exon	1	844	0.000000	+	.	gene_id "ERCC-00085"; transcript_id "DQ883669";
-ERCC-00086	ERCC	exon	1	1020	0.000000	+	.	gene_id "ERCC-00086"; transcript_id "DQ516791";
-ERCC-00092	ERCC	exon	1	1124	0.000000	+	.	gene_id "ERCC-00092"; transcript_id "DQ459425";
-ERCC-00095	ERCC	exon	1	521	0.000000	+	.	gene_id "ERCC-00095"; transcript_id "DQ516759";
-ERCC-00096	ERCC	exon	1	1107	0.000000	+	.	gene_id "ERCC-00096"; transcript_id "DQ459429";
-ERCC-00097	ERCC	exon	1	523	0.000000	+	.	gene_id "ERCC-00097"; transcript_id "DQ516758";
-ERCC-00098	ERCC	exon	1	1143	0.000000	+	.	gene_id "ERCC-00098"; transcript_id "DQ459415";
-ERCC-00099	ERCC	exon	1	1350	0.000000	+	.	gene_id "ERCC-00099"; transcript_id "DQ875387";
-ERCC-00104	ERCC	exon	1	2022	0.000000	+	.	gene_id "ERCC-00104"; transcript_id "DQ516815";
-ERCC-00108	ERCC	exon	1	1022	0.000000	+	.	gene_id "ERCC-00108"; transcript_id "DQ668365";
-ERCC-00109	ERCC	exon	1	536	0.000000	+	.	gene_id "ERCC-00109"; transcript_id "DQ854998";
-ERCC-00111	ERCC	exon	1	994	0.000000	+	.	gene_id "ERCC-00111"; transcript_id "DQ883685";
-ERCC-00112	ERCC	exon	1	1136	0.000000	+	.	gene_id "ERCC-00112"; transcript_id "DQ459422";
-ERCC-00113	ERCC	exon	1	840	0.000000	+	.	gene_id "ERCC-00113"; transcript_id "DQ883663";
-ERCC-00116	ERCC	exon	1	1991	0.000000	+	.	gene_id "ERCC-00116"; transcript_id "DQ668367";
-ERCC-00117	ERCC	exon	1	1136	0.000000	+	.	gene_id "ERCC-00117"; transcript_id "DQ459412";
-ERCC-00120	ERCC	exon	1	536	0.000000	+	.	gene_id "ERCC-00120"; transcript_id "DQ854992";
-ERCC-00123	ERCC	exon	1	1022	0.000000	+	.	gene_id "ERCC-00123"; transcript_id "DQ516782";
-ERCC-00126	ERCC	exon	1	1118	0.000000	+	.	gene_id "ERCC-00126"; transcript_id "DQ459427";
-ERCC-00130	ERCC	exon	1	1059	0.000000	+	.	gene_id "ERCC-00130"; transcript_id "EF011072";
-ERCC-00131	ERCC	exon	1	771	0.000000	+	.	gene_id "ERCC-00131"; transcript_id "DQ855003";
-ERCC-00134	ERCC	exon	1	274	0.000000	+	.	gene_id "ERCC-00134"; transcript_id "DQ516739";
-ERCC-00136	ERCC	exon	1	1033	0.000000	+	.	gene_id "ERCC-00136"; transcript_id "EF011063";
-ERCC-00137	ERCC	exon	1	537	0.000000	+	.	gene_id "ERCC-00137"; transcript_id "DQ855000";
-ERCC-00138	ERCC	exon	1	1024	0.000000	+	.	gene_id "ERCC-00138"; transcript_id "DQ516777";
-ERCC-00142	ERCC	exon	1	493	0.000000	+	.	gene_id "ERCC-00142"; transcript_id "DQ883646";
-ERCC-00143	ERCC	exon	1	784	0.000000	+	.	gene_id "ERCC-00143"; transcript_id "DQ668362";
-ERCC-00144	ERCC	exon	1	538	0.000000	+	.	gene_id "ERCC-00144"; transcript_id "DQ854995";
-ERCC-00145	ERCC	exon	1	1042	0.000000	+	.	gene_id "ERCC-00145"; transcript_id "DQ875386";
-ERCC-00147	ERCC	exon	1	1023	0.000000	+	.	gene_id "ERCC-00147"; transcript_id "DQ516790";
-ERCC-00148	ERCC	exon	1	494	0.000000	+	.	gene_id "ERCC-00148"; transcript_id "DQ883642";
-ERCC-00150	ERCC	exon	1	743	0.000000	+	.	gene_id "ERCC-00150"; transcript_id "DQ883659";
-ERCC-00154	ERCC	exon	1	537	0.000000	+	.	gene_id "ERCC-00154"; transcript_id "DQ854997";
-ERCC-00156	ERCC	exon	1	494	0.000000	+	.	gene_id "ERCC-00156"; transcript_id "DQ883643";
-ERCC-00157	ERCC	exon	1	1019	0.000000	+	.	gene_id "ERCC-00157"; transcript_id "DQ839618";
-ERCC-00158	ERCC	exon	1	1027	0.000000	+	.	gene_id "ERCC-00158"; transcript_id "DQ516795";
-ERCC-00160	ERCC	exon	1	743	0.000000	+	.	gene_id "ERCC-00160"; transcript_id "DQ883658";
-ERCC-00162	ERCC	exon	1	523	0.000000	+	.	gene_id "ERCC-00162"; transcript_id "DQ516750";
-ERCC-00163	ERCC	exon	1	543	0.000000	+	.	gene_id "ERCC-00163"; transcript_id "DQ668359";
-ERCC-00164	ERCC	exon	1	1022	0.000000	+	.	gene_id "ERCC-00164"; transcript_id "DQ516779";
-ERCC-00165	ERCC	exon	1	872	0.000000	+	.	gene_id "ERCC-00165"; transcript_id "DQ668363";
-ERCC-00168	ERCC	exon	1	1024	0.000000	+	.	gene_id "ERCC-00168"; transcript_id "DQ516776";
-ERCC-00170	ERCC	exon	1	1023	0.000000	+	.	gene_id "ERCC-00170"; transcript_id "DQ516773";
-ERCC-00171	ERCC	exon	1	505	0.000000	+	.	gene_id "ERCC-00171"; transcript_id "DQ854994";
diff --git a/workflows/host-genome-generation/test/fixtures/input.fasta b/workflows/host-genome-generation/test/fixtures/input.fasta
deleted file mode 100644
index 53a474ac2..000000000
--- a/workflows/host-genome-generation/test/fixtures/input.fasta
+++ /dev/null
@@ -1,100 +0,0 @@
->HiC_scaffold_1
-AAACGGAGCCCGCAGGGGAGCGGGGCGAGGGCCGCGGAGTCGTCCGTGTGACCGCGGCGGCCAGACCGGCGGGTCCTGCG
-CACCGGGCTTTGAACACGTCAAGCGACTTCACGACCAGCGCCACTCCCGCGCCACGAGGCCGGGCCCCCGTCACCGGCAG
-GACTTGGCCGGGCCCCAGAGCCGCGGGTTCGGCCGCGAGCTCAGCGGGGTGCCGCTCCAGCCCGGGACGCTGGTGGCCGA
-GCGGGCTGTGCCTTGGGCCCGGCCCAGAACTGGACGCTGCGGTCCGGGTCCGGAGGAGGGGGTGGGGGGCAGCGTGACGT
-TGGGGAAAGCTGACGACAGGGACGTAGCGGAGCGTGGCCAGGCTGGTGGCCTTGGTCAGCGCTGCAGGGTTCGGGGCCCA
-GCGTCCTCCCGCCGCCCTCACTGGTTCCGGGAAGGGCCTGGGGGCCGGACGTCGGGGTGAGGCAGCGCTGCTGGGCTCTG
-GGCACAAGGGACGGCAGGGACGGCAGGGACGATGGGGACTCCCCCCCACCCCCACATCTCCAGCCGGGGCTTGGTGTCCT
-CAGGTGCCACGTCCCTTCTGGGTGAGCCCCGTCCGGGCTGCGGCGGAGCAGGTGAGCAGAGAGGCCCCGGGCGCTCCAGG
-ACGGTGGCCGAAGGCGCGCGGGTTCCGCAGGATGAAAGTGGTTTTGCGGAGCCCGCGGCTGGTACCGCGGAGAGAAGGAG
-GCGGCGGAAGATCGTGCTCAGGAAATACGCCCTGGCGTTTGCAAAGGCGGTTCCTGCCGGCTTTACCTATCAGCAAATAC
-GAACCACGTTGTATTCACATTAATTTTTCTGTTGTCGGTAGTGCTAAAGCAACTGGTCTGTGAAGTGGATGGCAGTCTGT
-TTTGTTGGAAAATGGTAATTTTTATTATTTGAGGCCCAAACATAAACAAGTATTGTTTAAATACAGAAAAGATGATTTTA
-TCCTCTAAAACTTAATTTTTAAATCGTTGAATGGGTACTGATTTGCATGGATTAGAAATAAAAATCCTGAAAAGGTTCTC
-AGCGTAAAGTCTGCTTCCATCCCCCGCCTTCTCTGCGGGCCTCTATACCCCTCTGTGTGAGGCATTCTTACTGATGTTTT
-GGAACTCTTTATACATTGAGGATGTGAGATGTGATTAGCTTCTTGCGTACCCTTAAGAATTTCCTAATGCGTGTGTAAAC
-AAACATAAGTAGGTAGGCTCACTTTCACCCCCTCCCCCGTTTTTTAGACAAATAGTAGCATTATGGGTACAGGACTCCAC
-AGTATGTGGAGAATCTCCCATATATTAGTACATGGAGAACGTCTCCATTTTTTTAAAGCTACATCGTATTTCATTGTACG
-GATGTTTCTTATTGGTGGACACTTAAGTGGCTTCAGATTTTTTTGTCACAACAAATAATGCGCAAAAAGCCTTGCATAGA
-TGTCATTTTGCACATGTCTTTGGAATCAATCCCTAGGAGTAACATGCTCAAAGACTATGTCCCTTTGTGATTTTATAGCT
-GTTTTCGAATTATTCTACAAATGAGTTATAAATTTACTCCTCCAATATTTAAAAATGTTTCTATCTTCACACTTTAACTA
-TTGTAAAAATTTTTTGACTTTTGCCAATCTAATGTGTTTTTTTATTATTATTAATAAGGTTGAGCGTCTATTTGTCCCCC
-CACCCCCACCCCGCACTGGACTATCTAGTTAAAGTGTTTGCGCATTTATTTGGGTTGCTGATCTTTGTCCTTTTATTGAT
-TTTTAGGGGCTTTTTATATATTAAGGATATAGGGTGTGATAGATGGTGAAATATATTTTTCCCATTGTCTATCTTGATTT
-GTGAATATGCTGATGGCAGTTTCTTTCATGCAGAAGTTTTATTTTTCTGTAGTTTAATCTATAAATCCTTCATTTATCCA
-AATCTGGCATTTGGATTTTCAGTTTTAATTAGAAGAGTTTCTTTAACTACAGAGTTGTAATGAGAATCACTTGTGGTTTC
-TGTTAGTACTTTTATGATTTTATTTTTAATGCTTACATAATTGACCTATTCGGAATTTATTTCGATATACAGTGTGAGAT
-ATGGGTGCAACTCTTTTATTATTTTGCTGGATAGCTACTCAGTTGTCCTAATGCCATTTATCAGTCAATTTTTTTATTAT
-TTATTTGAGATGTCACCTTAAGTGTATAATACTTTCCTCACATATTTTGTGTCTACCTGTGCTTTCTATGTTTTTCTGTT
-GTTCTGTATGTCCATTCGTGCGTGAGCCAGCACTTCGGTATCAAGAATATTATATGATTTAGGAACTAGTAGGGCTACCT
-CCCTCTCTCAACTCTTTCTTTACAGAGTTTTTCTATTTTGTTTGTTTCTTTTTCTGTTTGAATTTTAGAATCAGATCGTC
-TAATCCTCACCCCATAATAAAACAATAAGGCACGAAGATAATAAAAACCTGGATTTTTATTATTTTTATTGAGGTTGCAT
-TAATTTATAAAAAAGTCAAGGAAATTGGCATTCTGGATATTGAATTTTCTTGTTGAATAGCATCATAAATCAACTTGTAC
-TAGTTTTCTTGTATGATTTTTTGAGGATATTTAAAAATGTTTCTCCTATTGATCTTCACTTCAGTCTATTCCTAGATACT
-TCCTCTTTGTTTTTGGCTAATTAAATGGAGCTGATTTCTTCCATTATATCTTCTAAAGCTATTGGTTTCTCTATATTAAT
-TTTATAACCTGATATCTTACTAAATTTATTATTTGTAGAAGATTTTCCCTCATTATCTTTGGGGATGAGATGGGTGTATC
-TTACCATGTTAAGAAAATATTTAATCTTTTTTTTTTTAATCAAAGTTTATAATGCTGAATTTTATTACTTTTTCAGCTTC
-TGTAAAGACGGTCCTATATTTTTATTCCTGGATCTGTTGAAAGATAAAACAAATGACCTGTAAGCAGCTGTTTAAGCCAG
-GCTTTTAGAAGTCTTTGTGTTTCACTTTGGCATATCCTCGCCGCTGTCTGTGGCAGGTGTCATTCAGAACCCAGGTCTCC
-ACGATCACCTTCTGTTTTCTGACATACTCGTAGCTCAACAGAATGTTGAATTCATTCAATAAAATATAGTAGAAAAAACA
-GAGCCGGTGCAGCCATGCCATTATTTCAAAGCTTACATTTTTGTCTCTGAATTTGGAAAATAATAGATATGTATTTCTTT
-AACGAAGAAAGCAATGTACAGTATGCCATCTTAAATCTGCGTGTGTGGATGGGTGGGCAGAGGTTGGTGTGTAGATAGGT
-AGCTTAGATGAAAATGAGGTTGGTAAATTTAAATTGACACGGTGCATACTTTTTACGCCCTTTTTAAAATGAAATAAGAA
-TTAAGAAAGCAAGTAAGTAGAAAATCAACGTCCACAGATGCCTACTCTTAAGATGGACCTGCCGGGCCGGTCTCCGTGGC
-AACGGCAGGGTGAGGGGGAAGGAGGACTGAGGAGAAGGTGTTTTTTTCTCTAAAACGCCTTCATTTCCTCAGCTTATTTA
-CTGCCTTTCAGTTCTACAGAATCACATTATGATTCTGTGGTGACTGGGAACCAAGAGCAGAAAATCATTTCTACCCCAAG
-GCACAGAGCAGGCACTTAGCATCAAAAGGAAGCAATCTGCAGGCTTTTGACAGCGTATTCACCTCCTGGGACTCGGGGTG
-GGGGCACAGGGACACCCATCCCTGTGTCTGGAGCCGTAAATCTCTAGCTGTGCATCCAGTGCCCATTTTTGGTGTTACGT
-GTGTCATGGAGGTGTCTTTAAATGCTCTGCAAACACTGACATCTGGGTTATTTATTTGTCTCCTCTGCGGAGAAGCTGGC
-AATAAACACATCACCCCAAAGCTGGGGAAGGCGGGCAGGAATGACCACATGGAAGAGCTATTAAATTGGTGACATTTTTC
-TTCCTACTGAGCCGGCGTCCATAAAACAACTGGACAGGGCCCACCTCCCCGCCAGACAGCAGTAACAGGCGGGTGACGGA
-TTGGATGTGGCGGGTGGAGCTCGGCTCCTGGGTTCCCTCAGGGACTTCCGATGGTCGCTCACTTTAGAGTTCATCTCTGT
-TTAAACTCCTCAGCGATTTCTTCCGCTGGCACAAGCTCTGAAGCTTGGGCGCCGCCGTCGTGCAGAAAGGGCCAGCCACA
-TTGACGCGACGGGAAGCCCTCGGCACGGCGCGGAGCTGGGGCCACCCTGCCGCTGGTGTTGTAGGGCTCCCCGATGTTTC
-TCAGAGGGCTTCCGGGGACCGCGGGCACACCGCCGCCCGGGAACCACCGGAAAGCCGCGTGTAGACGGGGCCGACGGCGA
-GGCCGGGCAGGGCCACTGCCCACCAGGAAGTGGCGGCCGCAGCACCAGGGTCTCGGTCCACTAAGGTCATGTGTTCACAG
-GAGCCTGGGAGGTGAGGGAACTGGGTGAGAACCTGCGGAAGCCACGGGGTGGGGGTGGGGGGCGGGGGTGCCCCGGGGGA
-GGGTGGCCCAGTGAAGGGCGGAGGTGGGGACACAGGTTGGCTTCTTGGGACTTTTAAAGGGCTGCTTCATAGGGGCGCCG
-TGGCCTGCCTGTGTGCGCGGGGGCTTGTGGGGCCACGCACCGCCGTCCCTCTGCGACCCAGCTCTGTCCCAGGCGCTGCA
-GGGAGCGTGACTGTGCCCCGTGGGGCCTGCGCCCCCTGGGGACCACCTGCACGCAGTCTGCCTCGACCCGTGAGCTCGGC
-CTCGAGACGGTGGTGGGCACTCCGGTCCAAGAGCTGAGTCCTGGCCTTTGGCTGGTTCCTGCAGGGACGATGTGGACTAG
-ACATCCAGGCCCGGACGGGACAGCCTGGGCAGGTCACAGGGGCCCGGGGACGGTGTGGAGCCAGCGTTGTTACTTACGGT
-GCAGAAAACAGCAAACTCGCCCTGCACGCGCTGCCATCAATTTGGCAGAGGCCGAGGAGGTGGTGACATGTTCATGTGTA
-AAGAAGGGGTCTGAAAACACTCACGGCAAAATGGGACTAATCTCCCTGACAGGTCCATGCCCAGCCGGAGGGACGCTGCC
-GGGTCACCCCCACCACACCCTGAGTCAGCGGGGTCGTCCCGGAACCGCAGGGGTCGGGGACCGCGAGGGGTGGCCCCGTG
-CGGAGCGCCCTGTCCGAGCAGGACGAGGCTTCCAGACCTGAGGGACAGCCGCGCCCCGCCCCTCCGAGGCTCCCTGAGGT
-GGAGCTGTGCGGGACAGCAGGTGGCCCCGTCTGGAAGGAGCTGCCGGAGCAGCAGCGACGCGGACAGTCGACTCCTGCCC
-GAGTCCGCCTTTCTCCCCCGAGCGTGCCGTGTGCCCGGCAGCCCCTGCCCCGCAGTCATGTCCTTTACCTGGTGTCCTCA
-GCAAACAGCCCTCCGTCACCGACACCATCAGTCTGTGCTGAACTGCGTATCCCCCGCCTTCCTGCCAGCTGCCCCCTCCC
-CAGCTTGTGACACTCTGCCCTGGTGGGCTCAGTATCCTGCCCGCAGACGCCCCGTGGAGCCCGAGTTCCCACGATGTCTG
-GCTGCTGTGTCTGGCGCCCTGTGCCTCGCGTGAAACCACTTTCTCCTGCGGAGGGTCCTGCTGGCACCCTCCCCTTGTCC
-TCCGGCTCATGGGGACAGTGCCCCGGCTGCTCTGACATCGGTCACTCTTGGTGCCGGGCCCGTGCTGTTCTGGGATGGTG
-GCGGGATGGGTCCTGGAATGTCACCACCGACCTATGGGAAGTTCAAAGTTTTGGGCCTCGGTTGCCTGTTGCTGATATGA
-TCTTTTTATTCATCTCAGATTTTCCATTTTTATCAGAAAGGGGATAAAGTTGCCTCTCTTGGCTTCTCTATTGTGAAAAC
-AAAGTAAATAGGATTAACATGTTTTAGCTTTTAGGAAGAATGGCATTTTCAAAATCTAAATAATTACTCTTAGGATGAAA
-GTTTTAGAACTTAGTTTTCCTTAGATTTATTGGTTATCATTAAATTAAAAATTTATTTTCTCAGAAACTCTACCCAATGT
-CTTGGATTCAAAGCTGGTTTCAGAAGCCAGAAGCCTATGTTTTGTGCTGAGAGTTCCCTGTAAACACCTGAGGACATTGG
-ACTCTTTTTGGGGGGGAACGAAACGAGCGTATTGTTGTTATTTTACCAGAACAGGAGAAAAACGCGGGAAGGTTTGTCCG
-GAACACGTGCTGGGCGAGGGAGAAGGGGTTGGGGCCTCAGCGCTGGGCGGGCAGAAGGAGGGGAGGCTGCGGGATCCCAC
-ACGGCTTCGGGGGCAGAGCCTGGCGGGCTGCGGCCCACGTAAGCGGCACCATCCGGCTCCGTGCCGGCCCCCGGCCCGGC
-AGCTGTCCCGCAGGATGCGCGGTGGCTGCCGCCCTGTCAGCCACCTCCTGCTCCCCCAGCTAGTGTGCTGACAGGCGTCC
-CAGACTGGGGGTGCTCACGCCGCAGCCAGGGGTCTTCGGAGTCACGGGAGTGTCACAGACCGCCGTCCAGACCCCACCTC
-CGGACGCCGAGTTCACGGCTCCGATCTCGTCTTAGGCCTTGATGCTGGTGGTTCTCGCTTTGTTTGGACATCAGTGTTTT
-TTAAAACTCGCCAGGGACCCAAATATGAAGCCAGGTTCGACTCACTGACGACGTCGGGCATTTCGGGGCCCCTAGGGCCT
-GGTCCTGGGACCGCACGTGACTCTGCAGCAAGAATGTCGTGTGGAGCCCCGTGCTGAGGTGGGAGGGGCAGGAGGGGTCA
-GGTGGCCGGAATGACTGGAGTCCACCCCACGTGCGTGTGAAGGGGAGCCAGGGGGCAGCGAGCACCTATGGAGGGCAGAG
-GACACGGTGTCATCATGTGGCTCGGCGGCACCGGCGGTGGCCCGGGCCAGGGTCACGGTGCAGACGGACCACACTCGAGA
-CCGAACGCCAGAGGACCGGCCACGGTGGAATCGGAGGCCGAGGGAAACTGATCAGGGAAGGCGGGGGCATCCGGAGCCAT
-GTCCACTGCATAACGGCAGCAGGAGCTGTGGGGGACGGCCCGGGCCCACTCACCGCGTCCGCTCACCGCCGAGTAGAGGT
-GCAAGCAGGAGGCCTGCGGGACACGAGTGGTGTGGCCGAGCGCCTGGAAGTCAGCCTGCGACAGAGTCCGTGGTCACTCA
-TCAGGCGAGAGGCTCAGGGAGGGGCCGCGCCGTCCCGGAGTCCCTGTGCCGATCACCGCGCCGTCCGGAGTCCCCGCGCC
-GATCACTGCGCCGTCCAGAGTCCCCGTGCCGATCACCGCGCCGTCCGGAGTCCCCGTGCTGATTGCCGCATTGTCCCAGA
-GTCCCTGTGCCGATCGCCACCGAGAGGTGGGAGCTGCTCCCACAGGTGCAGGAAGTGACACTGTGTTGCATCGCGTCAGG
-AGAGCGGCCCCGCGGACCTCCGCGTCCTTCGCGGCCAAGGCCAGCCGTGGGCCTCCCAGGCCCTGCTCAGAGATCACATG
-GTCCTAATTCGAAAGTAAAATTTTTGGAAAGAGATAAGCTTTAAACAATGATGAAATTTTTAAAAATCCCCCTAGATTTT
-CCAATTGCAACATTCTTGTAAGTTTGTCCAAACTGAACTTTTCCTCCCCCTGCGTCATGGTTGGCTTCGGATGTGCTCGC
-TTTGCTGGGTTCTGGGCAGGAGGTTTCGGGAGAGCTGGCTGGTCGCCGGGCTGGGCTGCGTCCCGCTAGATGTCCATGGG
-CAGAGCAACCGTTAAAACGAACGCGGTCCATGCCCACCCACTCACGCGCCCCAGAGAGTGGAGCCCGAGGGCACAGCCCA
-CAGACCGGCCCGGACCTCTGTCCCCGGCACGTGGGCTCCAGCTGAAGACACGGCCCCTGGGGCGTTGTGTCCTGGGTGCT
-GCCACCTAGGACGCTCCGGCCCAGCCAAGGAGACCCTCCTGCCACCAGCGAGGCCGTGTGGACGACCGGGCGCGCCTTGC
diff --git a/workflows/host-genome-generation/test/fixtures/input.fasta.gz b/workflows/host-genome-generation/test/fixtures/input.fasta.gz
new file mode 100644
index 0000000000000000000000000000000000000000..ff76d23ae80970788261ef97bd57a748f055f8b7
GIT binary patch
literal 2637
zcmV-T3bOSdiwFqMreb3N18Ht>b#yLfVRLk00DYOuie5(yg!lb6d4Yh?LVf`4O^7iV
z3|Zv;AxHI<`uxly<MGV==h7FcR4S?e{Pruq|NHk}KY#x7`^Wb`PDEr?RAyF2mHwVz
zS@UVG&ZW-h`}zO;3$D%g^TK@63(xI-{y3>CmEF&y@qBvj#EcowrTG~1TF%SanpJ<!
zY`i#M^Nt3NI(qTrW@xp{+36)dmpZ-j)}_`odMoDRT%Q|piuLKa8JVXTIp#s0PwlDv
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diff --git a/workflows/host-genome-generation/test/test_wdl.py b/workflows/host-genome-generation/test/test_wdl.py
index 8fe9ac77b..7935098d5 100644
--- a/workflows/host-genome-generation/test/test_wdl.py
+++ b/workflows/host-genome-generation/test/test_wdl.py
@@ -8,8 +8,8 @@ class TestIndexGeneration(WDLTestCase):
     wdl = os.path.join(os.path.dirname(__file__), "..", "host_genome_generation.wdl")
     common_inputs = {
         "genome_name": "test",
-        "genome_fasta_gz": os.path.join(os.path.dirname(__file__), "fixtures/input.fasta"),
-        "ERCC_fasta_gz": os.path.join(os.path.dirname(__file__), "fixtures/ERCC.fasta"),
+        "genome_fasta_gz": os.path.join(os.path.dirname(__file__), "fixtures/input.fa.gz"),
+        "ERCC_fasta_gz": os.path.join(os.path.dirname(__file__), "fixtures/ERCC.fa.gz"),
     }
 
     def testIndexGeneration(self):

From 29a721e798d1b8c327dbf8bcffa50c68d863fbcb Mon Sep 17 00:00:00 2001
From: morsecodist <todd@morsecodist.io>
Date: Thu, 2 Feb 2023 13:28:06 -0800
Subject: [PATCH 06/13] fix file naming

---
 .../test/fixtures/{ERCC.fasta.gz => ERCC.fa.gz}     | Bin
 .../test/fixtures/{input.fasta.gz => input.fa.gz}   | Bin
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename workflows/host-genome-generation/test/fixtures/{ERCC.fasta.gz => ERCC.fa.gz} (100%)
 rename workflows/host-genome-generation/test/fixtures/{input.fasta.gz => input.fa.gz} (100%)

diff --git a/workflows/host-genome-generation/test/fixtures/ERCC.fasta.gz b/workflows/host-genome-generation/test/fixtures/ERCC.fa.gz
similarity index 100%
rename from workflows/host-genome-generation/test/fixtures/ERCC.fasta.gz
rename to workflows/host-genome-generation/test/fixtures/ERCC.fa.gz
diff --git a/workflows/host-genome-generation/test/fixtures/input.fasta.gz b/workflows/host-genome-generation/test/fixtures/input.fa.gz
similarity index 100%
rename from workflows/host-genome-generation/test/fixtures/input.fasta.gz
rename to workflows/host-genome-generation/test/fixtures/input.fa.gz

From 99213603f0eb3e2481206925ee7c95c7c76e3cf6 Mon Sep 17 00:00:00 2001
From: morsecodist <todd@morsecodist.io>
Date: Thu, 2 Feb 2023 20:08:53 -0800
Subject: [PATCH 07/13] python path docker

---
 workflows/host-genome-generation/Dockerfile | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/workflows/host-genome-generation/Dockerfile b/workflows/host-genome-generation/Dockerfile
index d49538a1e..dc56abecd 100644
--- a/workflows/host-genome-generation/Dockerfile
+++ b/workflows/host-genome-generation/Dockerfile
@@ -2,9 +2,11 @@
 FROM ubuntu:22.04
 ARG DEBIAN_FRONTEND=noninteractive
 
-# This brings in python2.7
 RUN apt-get update && apt-get install -y wget bowtie2 curl minimap2 pigz dh-autoreconf nasm make git g++ unzip python3-pip
 
+# nescessary for hisat2
+RUN ln -s /usr/bin/python3 /usr/bin/python
+
 # Install STAR, the package rna-star does not include STARlong
 RUN curl -L https://github.com/alexdobin/STAR/archive/2.5.3a.tar.gz | tar xz
 RUN mv STAR-2.5.3a/bin/Linux_x86_64_static/* /usr/local/bin

From 315c39236f9fb14da4189d0730bc561a12ab33c4 Mon Sep 17 00:00:00 2001
From: morsecodist <todd@morsecodist.io>
Date: Thu, 2 Feb 2023 20:16:16 -0800
Subject: [PATCH 08/13] star gtf flag fix

---
 workflows/host-genome-generation/host_genome_generation.wdl | 1 -
 1 file changed, 1 deletion(-)

diff --git a/workflows/host-genome-generation/host_genome_generation.wdl b/workflows/host-genome-generation/host_genome_generation.wdl
index e6d08ac08..1da6f7e12 100644
--- a/workflows/host-genome-generation/host_genome_generation.wdl
+++ b/workflows/host-genome-generation/host_genome_generation.wdl
@@ -316,7 +316,6 @@ task star_generate {
     mkdir -p "$STAR_GENOME/part-0"
 
     STAR \
-      --sjdbGTFfile "~{transcripts_gtf_gz}" \
       --runThreadN ~{cpu} \
       --runMode genomeGenerate \
       --genomeFastaFiles "~{fasta}" \

From 06393711db61269bd90787e4da643010fbc07ff0 Mon Sep 17 00:00:00 2001
From: morsecodist <todd@morsecodist.io>
Date: Fri, 3 Feb 2023 19:07:46 -0800
Subject: [PATCH 09/13] syntax

---
 workflows/host-genome-generation/host_genome_generation.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/host-genome-generation/host_genome_generation.wdl b/workflows/host-genome-generation/host_genome_generation.wdl
index 1da6f7e12..3f85983b2 100644
--- a/workflows/host-genome-generation/host_genome_generation.wdl
+++ b/workflows/host-genome-generation/host_genome_generation.wdl
@@ -305,7 +305,7 @@ task star_generate {
     if [[ -n '~{transcripts_gtf_gz}' ]]; then
       transcripts_gtf="$TMPDIR/transcripts.gtf"
       pigz -dc '~{transcripts_gtf_gz}' > "$transcripts_gtf"
-      gtf_flag = "--sjdbGTFfile \"$transcripts_gtf\""
+      gtf_flag="--sjdbGTFfile \"$transcripts_gtf\""
     fi
 
     # Make directory for STAR genome

From 54d98fea93c73bad32c70935347939b9356a17cd Mon Sep 17 00:00:00 2001
From: morsecodist <todd@morsecodist.io>
Date: Fri, 3 Feb 2023 19:49:38 -0800
Subject: [PATCH 10/13] fix name outputs

---
 workflows/host-genome-generation/host_genome_generation.wdl | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/workflows/host-genome-generation/host_genome_generation.wdl b/workflows/host-genome-generation/host_genome_generation.wdl
index 3f85983b2..c76747af6 100644
--- a/workflows/host-genome-generation/host_genome_generation.wdl
+++ b/workflows/host-genome-generation/host_genome_generation.wdl
@@ -269,15 +269,15 @@ task minimap2_index {
     TMPDIR=${TMPDIR:-/tmp}
 
     if [ "~{nucleotide_type}" == "dna" ]; then
-        >&2 minimap2 -x map-ont -d '~{genome_name}_{nucleotide_type}.mmi' "~{fasta}"
+        >&2 minimap2 -x map-ont -d '~{genome_name}_~{nucleotide_type}.mmi' "~{fasta}"
     else
-        >&2 minimap2 -x splice -d '~{genome_name}_{nucleotide_type}.mmi' "~{fasta}"
+        >&2 minimap2 -x splice -d '~{genome_name}_~{nucleotide_type}.mmi' "~{fasta}"
     fi
     >&2 ls -l
   >>>
 
   output {
-      File index_mmi = "~{genome_name}_{nucleotide_type}.mmi"
+      File index_mmi = "~{genome_name}_~{nucleotide_type}.mmi"
   }
 
   runtime {

From 0d9277681dc42ae978a9820d45c2451d2515c33e Mon Sep 17 00:00:00 2001
From: rzlim08 <37033997+rzlim08@users.noreply.github.com>
Date: Wed, 5 Apr 2023 18:10:14 -0700
Subject: [PATCH 11/13] fix ercc gtf in host-genome generation (#202)

* fix ercc gtf in index generation

* pigz to cat
---
 .../host_genome_generation.wdl                       | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/workflows/host-genome-generation/host_genome_generation.wdl b/workflows/host-genome-generation/host_genome_generation.wdl
index c76747af6..98c7a2ec8 100644
--- a/workflows/host-genome-generation/host_genome_generation.wdl
+++ b/workflows/host-genome-generation/host_genome_generation.wdl
@@ -23,6 +23,7 @@ workflow host_filter_indexing {
 
     # ERCC sequences to spike in to the genome and transcript indexes
     File ERCC_fasta_gz
+    File? ERCC_fasta_gtf
 
     # Additional FASTA file(s) to spike into the Bowtie2 & HISAT2 indexes (e.g. EBV, phiX)
     # Sequence names must be unique among all FASTAs!
@@ -86,6 +87,7 @@ workflow host_filter_indexing {
   call star_generate {
     input:
     fasta = concatenate_and_unzip_fastas.fasta,
+    ERCC_fasta_gtf, 
     transcripts_gtf_gz,
     genome_name,
     docker_image_id,
@@ -289,6 +291,7 @@ task minimap2_index {
 task star_generate {
   input {
     File fasta
+    File? ERCC_fasta_gtf
     File? transcripts_gtf_gz
     String genome_name
 
@@ -302,10 +305,15 @@ task star_generate {
     TMPDIR=${TMPDIR:-/tmp}
 
     gtf_flag=""
-    if [[ -n '~{transcripts_gtf_gz}' ]]; then
+    if [[ -n '~{transcripts_gtf_gz}' || -n '~{ERCC_fasta_gtf}' ]]; then
       transcripts_gtf="$TMPDIR/transcripts.gtf"
-      pigz -dc '~{transcripts_gtf_gz}' > "$transcripts_gtf"
       gtf_flag="--sjdbGTFfile \"$transcripts_gtf\""
+      if [[ -n '~{transcripts_gtf_gz}' ]]; then
+        pigz -dc '~{transcripts_gtf_gz}' > "$transcripts_gtf"
+      fi 
+      if [[ -n '~{ERCC_fasta_gtf}' ]]; then
+        cat '~{ERCC_fasta_gtf}' >> "$transcripts_gtf"
+      fi 
     fi
 
     # Make directory for STAR genome

From 547a453217607a4802d99f742bb707f91be923ad Mon Sep 17 00:00:00 2001
From: rzlim08 <37033997+rzlim08@users.noreply.github.com>
Date: Wed, 26 Apr 2023 13:38:52 -0700
Subject: [PATCH 12/13] symlink bowtie2 directory (#229)

---
 workflows/host-genome-generation/host_genome_generation.wdl | 1 +
 1 file changed, 1 insertion(+)

diff --git a/workflows/host-genome-generation/host_genome_generation.wdl b/workflows/host-genome-generation/host_genome_generation.wdl
index 98c7a2ec8..3bb9a5c52 100644
--- a/workflows/host-genome-generation/host_genome_generation.wdl
+++ b/workflows/host-genome-generation/host_genome_generation.wdl
@@ -177,6 +177,7 @@ task bowtie2_build {
     mkdir -p "$TMPDIR"'/bt2/~{genome_name}'
     >&2 bowtie2-build --seed ~{seed} --threads ~{cpu} "~{fasta}" "$TMPDIR"'/bt2/~{genome_name}/~{genome_name}'
     >&2 ls -lR "$TMPDIR/bt2"
+    ln -s "$TMPDIR"'/bt2/~{genome_name}' "$TMPDIR"'/bt2/~{genome_name}.bowtie2'
     env -C "$TMPDIR/bt2" tar c . > '~{genome_name}.bowtie2.tar'
   >>>
 

From a9a57a4865c0a29f25e81ffe7daa83f85fa859be Mon Sep 17 00:00:00 2001
From: rzlim08 <37033997+rzlim08@users.noreply.github.com>
Date: Tue, 23 May 2023 09:29:25 -0700
Subject: [PATCH 13/13] create a relative symlink (#250)

---
 workflows/host-genome-generation/host_genome_generation.wdl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/host-genome-generation/host_genome_generation.wdl b/workflows/host-genome-generation/host_genome_generation.wdl
index 3bb9a5c52..8faaa4a4c 100644
--- a/workflows/host-genome-generation/host_genome_generation.wdl
+++ b/workflows/host-genome-generation/host_genome_generation.wdl
@@ -177,7 +177,7 @@ task bowtie2_build {
     mkdir -p "$TMPDIR"'/bt2/~{genome_name}'
     >&2 bowtie2-build --seed ~{seed} --threads ~{cpu} "~{fasta}" "$TMPDIR"'/bt2/~{genome_name}/~{genome_name}'
     >&2 ls -lR "$TMPDIR/bt2"
-    ln -s "$TMPDIR"'/bt2/~{genome_name}' "$TMPDIR"'/bt2/~{genome_name}.bowtie2'
+    ln -r -s "$TMPDIR"'/bt2/~{genome_name}' "$TMPDIR"'/bt2/~{genome_name}.bowtie2'
     env -C "$TMPDIR/bt2" tar c . > '~{genome_name}.bowtie2.tar'
   >>>