Build branch main with version main (0c8a7eb)

Build pipeline: viash-hub.rnaseq.main-nn8dl

Source commit: 0c8a7eb648

Source message: remove citation

target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml

@@ -459,51 +459,57 @@ dependencies:
 - name: "star/star_align_reads"
   repository:
     type: "vsh"
-    repo: "vsh/biobox"
+    repo: "biobox"
     tag: "main"
 - name: "samtools/samtools_sort"
   repository:
     type: "vsh"
-    repo: "vsh/biobox"
+    repo: "biobox"
     tag: "main"
 - name: "samtools/samtools_index"
   repository:
     type: "vsh"
-    repo: "vsh/biobox"
+    repo: "biobox"
     tag: "main"
 - name: "samtools/samtools_stats"
   repository:
     type: "vsh"
-    repo: "vsh/biobox"
+    repo: "biobox"
     tag: "main"
 - name: "samtools/samtools_flagstat"
   repository:
     type: "vsh"
-    repo: "vsh/biobox"
+    repo: "biobox"
     tag: "main"
 - name: "samtools/samtools_idxstats"
   repository:
     type: "vsh"
-    repo: "vsh/biobox"
+    repo: "biobox"
     tag: "main"
-- name: "umitools/umitools_dedup"
+- name: "umi_tools/umi_tools_dedup"
   repository:
-    type: "local"
-- name: "umitools_prepareforquant"
+    type: "vsh"
+    repo: "biobox"
+    tag: "main"
+- name: "umi_tools/umi_tools_prepareforrsem"
   repository:
-    type: "local"
+    type: "vsh"
+    repo: "biobox"
+    tag: "main"
 - name: "salmon/salmon_quant"
   repository:
     type: "vsh"
-    repo: "vsh/biobox"
+    repo: "biobox"
     tag: "main"
 - name: "rsem/rsem_calculate_expression"
   repository:
-    type: "local"
+    type: "vsh"
+    repo: "biobox"
+    tag: "main"
 repositories:
 - type: "vsh"
   name: "biobox"
-  repo: "vsh/biobox"
+  repo: "biobox"
   tag: "main"
 - type: "vsh"
   name: "craftbox"
@@ -584,8 +590,8 @@ build_info:
   output: "target/executable/workflows/genome_alignment_and_quant"
   executable: "target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant"
   viash_version: "0.9.0"
-  git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
-  git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
+  git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b"
+  git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads"
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort"
@@ -593,10 +599,10 @@ build_info:
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats"
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat"
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats"
-  - "target/nextflow/umitools/umitools_dedup"
-  - "target/nextflow/umitools_prepareforquant"
+  - "target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_dedup"
+  - "target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_prepareforrsem"
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant"
-  - "target/nextflow/rsem/rsem_calculate_expression"
+  - "target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_calculate_expression"
 package_config:
   name: "rnaseq"
   version: "main"
@@ -607,7 +613,7 @@ package_config:
   repositories:
   - type: "vsh"
     name: "biobox"
-    repo: "vsh/biobox"
+    repo: "biobox"
     tag: "main"
   - type: "vsh"
     name: "craftbox"

target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant

@@ -1285,16 +1285,16 @@ fi
 
 
 # set dependency paths
-VIASH_DEP_UMITOOLS_UMITOOLS_DEDUP="$VIASH_META_RESOURCES_DIR/../../../nextflow/umitools/umitools_dedup/main.nf"
-VIASH_DEP_UMITOOLS_PREPAREFORQUANT="$VIASH_META_RESOURCES_DIR/../../../nextflow/umitools_prepareforquant/main.nf"
-VIASH_DEP_RSEM_RSEM_CALCULATE_EXPRESSION="$VIASH_META_RESOURCES_DIR/../../../nextflow/rsem/rsem_calculate_expression/main.nf"
 VIASH_DEP_STAR_STAR_ALIGN_READS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf"
 VIASH_DEP_SAMTOOLS_SAMTOOLS_SORT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf"
 VIASH_DEP_SAMTOOLS_SAMTOOLS_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf"
 VIASH_DEP_SAMTOOLS_SAMTOOLS_STATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf"
 VIASH_DEP_SAMTOOLS_SAMTOOLS_FLAGSTAT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf"
 VIASH_DEP_SAMTOOLS_SAMTOOLS_IDXSTATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf"
+VIASH_DEP_UMI_TOOLS_UMI_TOOLS_DEDUP="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_dedup/main.nf"
+VIASH_DEP_UMI_TOOLS_UMI_TOOLS_PREPAREFORRSEM="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_prepareforrsem/main.nf"
 VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf"
+VIASH_DEP_RSEM_RSEM_CALCULATE_EXPRESSION="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_calculate_expression/main.nf"
 
 ViashDebug "Running command: $(echo $VIASH_CMD)"
 cat << VIASHEOF | eval $VIASH_CMD
@@ -1400,167 +1400,169 @@ workflow run_wf {
           key: "genome_idxstats"
       )
 
-      //
-      // Remove duplicate reads from BAM file based on UMIs
-      // 
-      
-      // Deduplicate genome BAM file
-      | umitools_dedup.run ( 
-          runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
-          fromState: [
-            "paired": "paired", 
-            "bam": "genome_bam_sorted", 
-            "bai": "genome_bam_index",
-            "get_output_stats": "umi_dedup_stats"
-          ],
-          toState: [ "genome_bam_sorted": "output_bam" ],
-          key: "genome_deduped"
-      )
-      | samtools_index.run (
-          runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
-          fromState: [
-            "input": "genome_bam_sorted", 
-            "csi": "bam_csi_index"
-          ],
-          toState: [ "genome_bam_index": "output" ],
-          key: "genome_deduped"
-      )
-      | samtools_stats.run (
-          runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
-          fromState: [
-            "input": "genome_bam_sorted", 
-            "bai": "genome_bam_index", 
-            "fasta": "fasta"
-          ],
-          toState: [ "genome_bam_stats": "output" ],
-          key: "genome_deduped_stats"
-      )
-      | samtools_flagstat.run (
-          runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
-          fromState: [
-            "bam": "genome_bam_sorted", 
-            "bai": "genome_bam_index", 
-            "fasta": "fasta"
-          ],
-          toState: [ "genome_bam_flagstat": "output" ],
-          key: "genome_deduped_flagstat"
-      )
-      | samtools_idxstats.run(
-          runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
-          fromState: [
-            "bam": "genome_bam_sorted", 
-            "bai": "genome_bam_index", 
-            "fasta": "fasta", 
-          ],
-          toState: [ "genome_bam_idxstats": "output" ],
-          key: "genome_deduped_idxstats"
-      )
+    //
+    // Remove duplicate reads from BAM file based on UMIs
+    // 
+    
+    // Deduplicate genome BAM file
+    | umi_tools_dedup.run ( 
+        runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
+        fromState: { id, state -> 
+          def output_stats = state.umi_dedup_stats ? state.id : 
+          [ paired: state.paired, 
+          input: state.genome_bam, 
+          bai: state.genome_bam_index,
+          output_stats: output_stats] 
+        },
+        toState: [ "genome_bam_sorted": "output" ],
+        key: "genome_deduped"
+    )
+    | samtools_index.run (
+        runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
+        fromState: [
+          "input": "genome_bam_sorted", 
+          "csi": "bam_csi_index"
+        ],
+        toState: [ "genome_bam_index": "output" ],
+        key: "genome_deduped"
+    )
+    | samtools_stats.run (
+        runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
+        fromState: [
+          "input": "genome_bam_sorted", 
+          "bai": "genome_bam_index", 
+          "fasta": "fasta"
+        ],
+        toState: [ "genome_bam_stats": "output" ],
+        key: "genome_deduped_stats"
+    )
+    | samtools_flagstat.run (
+        runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
+        fromState: [
+          "bam": "genome_bam_sorted", 
+          "bai": "genome_bam_index", 
+          "fasta": "fasta"
+        ],
+        toState: [ "genome_bam_flagstat": "output" ],
+        key: "genome_deduped_flagstat"
+    )
+    | samtools_idxstats.run(
+        runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
+        fromState: [
+          "bam": "genome_bam_sorted", 
+          "bai": "genome_bam_index", 
+          "fasta": "fasta", 
+        ],
+        toState: [ "genome_bam_idxstats": "output" ],
+        key: "genome_deduped_idxstats"
+    )
 
       // Deduplicate transcriptome BAM file
 
-      | samtools_sort.run (
-          runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
-          fromState: [ "input": "transcriptome_bam" ],
-          toState: [ "transcriptome_bam": "output" ],
-          key: "transcriptome_sorted"
-      )
-      | samtools_index.run (
-          runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
-          fromState: [
-            "input": "transcriptome_bam", 
-            "csi": "bam_csi_index"
-          ],
-          toState: [ "transcriptome_bam_index": "output" ],
-          key: "transcriptome_sorted"
-      )
-      | samtools_stats.run (
-          runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
-          fromState: [
-            "input": "transcriptome_bam", 
-            "bai": "transcriptome_bam_index", 
-          ],
-          toState: [ "transcriptome_bam_stats": "output" ],
-          key: "transcriptome_stats"
-      )
-      | samtools_flagstat.run (
-          runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
-          fromState: [
-            "bam": "transcriptome_bam", 
-            "bai": "transcriptome_bam_index"
-          ],
-          toState: [ "transcriptome_bam_flagstat": "output" ],
-          key: "transcriptome_flagstat"
-      )
-      | samtools_idxstats.run(
-          runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
-          fromState: [
-            "bam": "transcriptome_bam", 
-            "bai": "transcriptome_bam_index" 
-          ],
-          toState: [ "transcriptome_bam_idxstats": "output" ],
-          key: "transcriptome_idxstats"
-      )    
-      
-      | umitools_dedup.run ( 
-          runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
-          fromState: [
-            "paired": "paired", 
-            "bam": "transcriptome_bam", 
-            "bai": "transcriptome_bam_index",
-            "get_output_stats": "umi_dedup_stats", 
-          ],
-          toState: [ "transcriptome_bam_deduped": "output_bam" ],
-          key: "transcriptome_deduped"
-      )
-      | samtools_sort.run (
-          runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, 
-          fromState: [ "input": "transcriptome_bam_deduped" ],
-          toState: [ "transcriptome_bam": "output" ],
-          key: "transcriptome_deduped_sorted"
-      )
-      | samtools_index.run (
+    | samtools_sort.run (
+        runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
+        fromState: [ "input": "transcriptome_bam" ],
+        toState: [ "transcriptome_bam": "output" ],
+        key: "transcriptome_sorted"
+    )
+    | samtools_index.run (
         runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
         fromState: [
           "input": "transcriptome_bam", 
           "csi": "bam_csi_index"
         ],
         toState: [ "transcriptome_bam_index": "output" ],
+        key: "transcriptome_sorted"
+    )
+    | samtools_stats.run (
+        runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
+        fromState: [
+          "input": "transcriptome_bam", 
+          "bai": "transcriptome_bam_index", 
+        ],
+        toState: [ "transcriptome_bam_stats": "output" ],
+        key: "transcriptome_stats"
+    )
+    | samtools_flagstat.run (
+        runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
+        fromState: [
+          "bam": "transcriptome_bam", 
+          "bai": "transcriptome_bam_index"
+        ],
+        toState: [ "transcriptome_bam_flagstat": "output" ],
+        key: "transcriptome_flagstat"
+    )
+    | samtools_idxstats.run(
+        runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
+        fromState: [
+          "bam": "transcriptome_bam", 
+          "bai": "transcriptome_bam_index" 
+        ],
+        toState: [ "transcriptome_bam_idxstats": "output" ],
+        key: "transcriptome_idxstats"
+    )    
+     
+    | umi_tools_dedup.run ( 
+        runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
+        fromState: { id, state -> 
+          def output_stats = state.umi_dedup_stats ? state.id : 
+          [ paired: state.paired, 
+          input: state.transcriptome_bam, 
+          bai: state.transcriptome_bam_index,
+          output_stats: output_stats] 
+        },
+        toState: [ "transcriptome_bam_deduped": "output" ],
+        key: "transcriptome_deduped"
+    )
+    | samtools_sort.run (
+        runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, 
+        fromState: [ "input": "transcriptome_bam_deduped" ],
+        toState: [ "transcriptome_bam": "output" ],
         key: "transcriptome_deduped_sorted"
-      )
-      | samtools_stats.run (
-          runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, 
-          fromState: [
-            "input": "transcriptome_bam", 
-            "bai": "transcriptome_bam_index"
-          ],
-          toState: [ "transcriptome_bam_stats": "output" ],
-          key: "transcriptome_deduped_stats"
-      )
-      | samtools_flagstat.run (
-          runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, 
-          fromState: [
-            "bam": "transcriptome_bam", 
-            "bai": "transcriptome_bam_index"
-          ],
-          toState: [ "transcriptome_bam_flagstat": "output" ],
-          key: "transcriptome_deduped_flagstat"
-      )
-      | samtools_idxstats.run(
-          runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, 
-          fromState: [
-            "bam": "transcriptome_bam", 
-            "bai": "transcriptome_bam_index" 
-          ],
-          toState: [ "transcriptome_bam_idxstats": "output" ],
-          key: "transcriptome_deduped_idxstats"
-      ) 
+    )
+    | samtools_index.run (
+      runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
+      fromState: [
+        "input": "transcriptome_bam", 
+        "csi": "bam_csi_index"
+      ],
+      toState: [ "transcriptome_bam_index": "output" ],
+      key: "transcriptome_deduped_sorted"
+    )
+    | samtools_stats.run (
+        runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, 
+        fromState: [
+          "input": "transcriptome_bam", 
+          "bai": "transcriptome_bam_index"
+        ],
+        toState: [ "transcriptome_bam_stats": "output" ],
+        key: "transcriptome_deduped_stats"
+    )
+    | samtools_flagstat.run (
+        runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, 
+        fromState: [
+          "bam": "transcriptome_bam", 
+          "bai": "transcriptome_bam_index"
+        ],
+        toState: [ "transcriptome_bam_flagstat": "output" ],
+        key: "transcriptome_deduped_flagstat"
+    )
+    | samtools_idxstats.run(
+        runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, 
+        fromState: [
+          "bam": "transcriptome_bam", 
+          "bai": "transcriptome_bam_index" 
+        ],
+        toState: [ "transcriptome_bam_idxstats": "output" ],
+        key: "transcriptome_deduped_idxstats"
+    ) 
 
-      // Fix paired-end reads in name sorted BAM file
-      | umitools_prepareforquant.run (
-          runIf: { id, state -> state.with_umi && state.paired && state.aligner == 'star_salmon' },
-          fromState: [ "bam": "transcriptome_bam" ],
-          toState: [ "transcriptome_bam": "output" ]
-      )
+    // Fix paired-end reads in name sorted BAM file
+    | umi_tools_prepareforrsem.run (
+        runIf: { id, state -> state.with_umi && state.paired && state.aligner == 'star_salmon' },
+        fromState: [ "input": "transcriptome_bam" ],
+        toState: [ "transcriptome_bam": "output" ]
+    )
 
       // Infer lib-type for salmon quant
       | map { id, state -> 
@@ -1597,78 +1599,91 @@ workflow run_wf {
           ]
       )
 
-      | map { id, state -> 
-        def mod_state = (state.aligner == 'star_salmon') ? state + [salmon_multiqc: state.quant_out_dir] : state
-        [ id, mod_state ]
-      }
-    
-      | rsem_calculate_expression.run (
-          runIf: { id, state -> state.aligner == 'star_rsem' },
-          fromState: [
-            "id": "id",
-            "strandedness": "strandedness",
-            "paired": "paired",
-            "input": "input",
-            "index": "rsem_index",
-            "extra_args": "extra_rsem_calculate_expression_args"
-          ],
-          toState: [
-            "rsem_counts_gene": "counts_gene",
-            "rsem_counts_transcripts": "counts_transcripts",
-            "rsem_multiqc": "stat",
-            "star_multiqc": "logs",
-            "bam_star_rsem": "bam_star",
-            "bam_genome_rsem": "bam_genome",
-            "bam_transcript_rsem": "bam_transcript"
-          ]
-      )
-    
-      // RSEM_Star BAM
-      | samtools_sort.run (
-          runIf: { id, state -> state.aligner == 'star_rsem' },
-          fromState: ["input": "bam_star_rsem"],
-          toState: ["genome_bam_sorted": "output"],
-          key: "genome_sorted"
-      )
-      | samtools_index.run (
-          runIf: { id, state -> state.aligner == 'star_rsem' },
-          fromState: [ 
-            "input": "genome_bam_sorted", 
-            "csi": "bam_csi_index"
-          ],
-          toState: [ "genome_bam_index": "output" ],
-          key: "genome_sorted"
-      )
-      | samtools_stats.run (
-          runIf: { id, state -> state.aligner == 'star_rsem' },
-          fromState: [
-            "input": "genome_bam_sorted", 
-            "bai": "genome_bam_index", 
-            "fasta": "fasta"
-          ],
-          toState: [ "genome_bam_stats": "output" ],
-          key: "genome_stats"
-      )
-      | samtools_flagstat.run (
-          runIf: { id, state -> state.aligner == 'star_rsem' },
-          fromState: [
-            "bam": "genome_bam_sorted", 
-            "bai": "genome_bam_index", 
-            "fasta": "fasta" 
-          ],
-          toState: [ "genome_bam_flagstat": "output" ],
-          key: "genome_flagstat"
-      )
-      | samtools_idxstats.run(
-          runIf: { id, state -> state.aligner == 'star_rsem' },
-          fromState: [
-            "bam": "genome_bam_sorted", 
-            "bai": "genome_bam_index", 
-            "fasta": "fasta" 
-          ],
-          toState: [ "genome_bam_idxstats": "output" ],
-          key: "genome_idxstats"
-      )
+    | map { id, state -> 
+      def mod_state = (state.aligner == 'star_salmon') ? state + [salmon_multiqc: state.quant_out_dir] : state
+      [ id, mod_state ]
+    }
+  
+    | rsem_calculate_expression.run (
+        runIf: { id, state -> state.aligner == 'star_rsem' },
+        fromState: [
+          "id": "id",
+          "strandedness": "strandedness",
+          "paired": "paired",
+          "input": "input",
+          "index": "rsem_index", 
+          "counts_gene": "rsem_counts_gene",
+          "counts_transcripts": "rsem_counts_transcripts",
+          "stat": "rsem_multiqc",
+          "logs": "star_multiqc",
+          "bam_star": "bam_star_rsem",
+          "bam_genome": "bam_genome_rsem",
+          "bam_transcript": "bam_transcript_rsem"          
+        ],
+        args: [
+          star: true,
+          star_output_genome_bam: true,
+          star_gzipped_read_file: true,
+          estimate_rspd: true,
+          seed: 1
+        ],
+        toState: [
+          "rsem_counts_gene": "counts_gene",
+          "rsem_counts_transcripts": "counts_transcripts",
+          "rsem_multiqc": "stat",
+          "star_multiqc": "logs",
+          "bam_star_rsem": "bam_star",
+          "bam_genome_rsem": "bam_genome",
+          "bam_transcript_rsem": "bam_transcript"
+        ]
+    )
+   
+    // RSEM_Star BAM
+    | samtools_sort.run (
+        runIf: { id, state -> state.aligner == 'star_rsem' },
+        fromState: ["input": "bam_star_rsem"],
+        toState: ["genome_bam_sorted": "output"],
+        key: "genome_sorted"
+    )
+    | samtools_index.run (
+        runIf: { id, state -> state.aligner == 'star_rsem' },
+        fromState: [ 
+          "input": "genome_bam_sorted", 
+          "csi": "bam_csi_index"
+        ],
+        toState: [ "genome_bam_index": "output" ],
+        key: "genome_sorted"
+    )
+    | samtools_stats.run (
+        runIf: { id, state -> state.aligner == 'star_rsem' },
+        fromState: [
+          "input": "genome_bam_sorted", 
+          "bai": "genome_bam_index", 
+          "fasta": "fasta"
+        ],
+        toState: [ "genome_bam_stats": "output" ],
+        key: "genome_stats"
+    )
+    | samtools_flagstat.run (
+        runIf: { id, state -> state.aligner == 'star_rsem' },
+        fromState: [
+          "bam": "genome_bam_sorted", 
+          "bai": "genome_bam_index", 
+          "fasta": "fasta" 
+        ],
+        toState: [ "genome_bam_flagstat": "output" ],
+        key: "genome_flagstat"
+    )
+    | samtools_idxstats.run(
+        runIf: { id, state -> state.aligner == 'star_rsem' },
+        fromState: [
+          "bam": "genome_bam_sorted", 
+          "bai": "genome_bam_index", 
+          "fasta": "fasta" 
+        ],
+        toState: [ "genome_bam_idxstats": "output" ],
+        key: "genome_idxstats"
+    )
 
       | map { id, state -> 
         def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }