add ss param for rnaspades

nf-core · Jul 15, 2024 · 7afedf2 · 7afedf2
1 parent 6e8e50b
commit 7afedf2
Show file tree

Hide file tree

Showing 6 changed files with 92 additions and 28 deletions.
diff --git a/docs/usage.md b/docs/usage.md
@@ -127,7 +127,7 @@ assemblers/methods/outputs to want to include as inputs to Evidential Gene:
 - `--soft_filtered_transcripts` (to include soft filtered transcripts from rnaSPAdes as inputs to Evidential Gene)
 - `--hard_filtered_transcripts` (to include hard filtered transcripts from rnaSPAdes as inputs to Evidential Gene)
 
-Extra parameters can be provided to Trinity using the `extra_trinity_args` parameter.
+Extra parameters can be provided to Trinity using the `extra_trinity_args` parameter. The `ss` param can be used to set the strand-specific type for rnaSPAdes.
 
 All assemblies are concatenated into one and redundancy is reduced using
 Evidential Gene's tr2aacds tool. You can provide additional parameters to tr2aacds

diff --git a/modules.json b/modules.json
@@ -8,71 +8,99 @@
                     "busco/busco": {
                         "branch": "master",
                         "git_sha": "17486961b8b1ab1aae258c83a7e947b40d8ab670",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "cat/cat": {
                         "branch": "master",
                         "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "cat/fastq": {
                         "branch": "master",
                         "git_sha": "4fc983ad0b30e6e32696fa7d980c76c7bfe1c03e",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "evigene/tr2aacds": {
                         "branch": "master",
                         "git_sha": "95d52841a6e2c6cd789dfd7248ac12a0fe4b5501",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "fastp": {
                         "branch": "master",
                         "git_sha": "95cf5fe0194c7bf5cb0e3027a2eb7e7c89385080",
-                        "installed_by": ["fastq_trim_fastp_fastqc", "modules"]
+                        "installed_by": [
+                            "fastq_trim_fastp_fastqc",
+                            "modules"
+                        ]
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
-                        "installed_by": ["fastq_trim_fastp_fastqc", "modules"]
+                        "installed_by": [
+                            "fastq_trim_fastp_fastqc",
+                            "modules"
+                        ]
                     },
                     "gawk": {
                         "branch": "master",
                         "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "salmon/index": {
                         "branch": "master",
                         "git_sha": "cb6b2b94fc40dea58f0b1e3dd095f3dd24f2ac8a",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/salmon/index/salmon-index.diff"
                     },
                     "salmon/quant": {
                         "branch": "master",
                         "git_sha": "727232afb8294b53dd9d05bfe469b70cce1675bb",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/salmon/quant/salmon-quant.diff"
                     },
                     "sortmerna": {
                         "branch": "master",
                         "git_sha": "ad22467dff16284093e7335d5e77964e9bbc510b",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/sortmerna/sortmerna.diff"
                     },
                     "spades": {
                         "branch": "master",
                         "git_sha": "b3f04d8392f4571d5869eb3a345892dd2cbea225",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/spades/spades.diff"
                     },
                     "trinity": {
                         "branch": "master",
                         "git_sha": "e06c5f45395d6e34531257b125d410a298a3bd4f",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/trinity/trinity.diff"
                     }
                 }
@@ -82,25 +110,33 @@
                     "fastq_trim_fastp_fastqc": {
                         "branch": "master",
                         "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
                         "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "utils_nfvalidation_plugin": {
                         "branch": "master",
                         "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     }
                 }
             }
         }
     }
-}
+}
diff --git a/modules/nf-core/spades/main.nf b/modules/nf-core/spades/main.nf
diff --git a/modules/nf-core/spades/spades.diff b/modules/nf-core/spades/spades.diff
diff --git a/nextflow.config b/nextflow.config
@@ -38,6 +38,7 @@ params {
     rnaspades                  = true
     soft_filtered_transcripts  = false
     hard_filtered_transcripts  = false
+    ss                         = null
     extra_tr2aacds_args        = null
 
     // BUSCO options

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -13,13 +13,11 @@
             "properties": {
                 "QC_only": {
                     "type": "boolean",
-                    "description": "Whether the pipeline should only perform quality control, and skip assembly and quantification.",
-                    "default": false
+                    "description": "Whether the pipeline should only perform quality control, and skip assembly and quantification."
                 },
                 "skip_assembly": {
                     "type": "boolean",
-                    "description": "Whether the pipeline should skip assembly steps, and only perform quality control of reads and quantification. --transcript_fasta must be provided if True.",
-                    "default": false
+                    "description": "Whether the pipeline should skip assembly steps, and only perform quality control of reads and quantification. --transcript_fasta must be provided if True."
                 }
             },
             "fa_icon": "fas fa-angle-double-right"
@@ -159,6 +157,11 @@
                     "type": "boolean",
                     "description": "For including soft filtered transcripts (in addition to the medium filtered transcripts) from rnaSPAdes in the input to EvidentialGene tr2aacds."
                 },
+                "ss": {
+                    "type": "string",
+                    "description": "Set strand-specific type for rnaSPAdes. Use `--ss rf` when first read in pair corresponds to reverse gene strand (antisense data, e.g. obtained via dUTP protocol) and `--ss fr` otherwise (forward).",
+                    "help_text": "Note, that strand-specificity is not related and should not be confused with FR and RF orientation of paired reads. RNA-Seq paired-end reads typically have forward-reverse orientation (--> <--), which is assumed by default and no additional options are needed."
+                },
                 "extra_tr2aacds_args": {
                     "type": "string",
                     "description": "Extra arguments for tr2aacds.pl. For example, '-MINAA=20'"