[skip ci] removed kallisto strandedness as a standalone parameter

Author: pinin4fjords

docs/usage.md

@@ -67,7 +67,7 @@ By default, the pipeline uses [STAR](https://github.com/alexdobin/STAR) (i.e. `-
 
 You also have the option to pseudoalign and quantify your data directly with [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html) or [Kallisto](https://pachterlab.github.io/kallisto/) by specifying `salmon` or `kallisto` to the `--pseudo_aligner` parameter. The selected pseudoaligner will then be run in addition to the standard alignment workflow defined by `--aligner`, mainly because it allows you to obtain QC metrics with respect to the genomic alignments. However, you can provide the `--skip_alignment` parameter if you would like to run Salmon or Kallisto in isolation. By default, the pipeline will use the genome fasta and gtf file to generate the transcripts fasta file, and then to build the Salmon index. You can override these parameters using the `--transcript_fasta` and `--salmon_index` parameters, respectively.
 
-The library preparation protocol (library type) used by Salmon quantification is inferred by the pipeline based on the information provided in the samplesheet, however, you can override it using the `--salmon_quant_libtype` parameter. You can find the available options in the [Salmon documentation](https://salmon.readthedocs.io/en/latest/library_type.html). Similarly, strandedness is taken from the sample sheet or calculated automatically, and passed to Kallisto on a per-library basis, but you can apply a global override by setting `--kallisto_quant_strandedness` see the [Kallisto documentation](https://pachterlab.github.io/kallisto/manual).
+The library preparation protocol (library type) used by Salmon quantification is inferred by the pipeline based on the information provided in the samplesheet, however, you can override it using the `--salmon_quant_libtype` parameter. You can find the available options in the [Salmon documentation](https://salmon.readthedocs.io/en/latest/library_type.html). Similarly, strandedness is taken from the sample sheet or calculated automatically, and passed to Kallisto on a per-library basis, but you can apply a global override by setting the Kallisto strandedness parameters in `--extra_kallisto_quant_args` like `--extra_kallisto_quant_args '--fr-stranded'` see the [Kallisto documentation](https://pachterlab.github.io/kallisto/manual).
 
 When running Salmon in mapping-based mode via `--pseudo_aligner salmon` the entire genome of the organism is used by default for the decoy-aware transcriptome when creating the indices (see second bulleted option in [Salmon documentation](https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode)).
 
@@ -93,9 +93,9 @@ The `--umitools_grouping_method` parameter affects [how similar, but non-identic
 
 #### Examples:
 
-| UMI type     | Source                                                                                                                                                                                                                                               | Pipeline parameters                                                                                                                            |
-| ------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------- |
-| In read name | [Illumina BCL convert >3.7.5](https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl_convert/bcl-convert-v3-7-5-software-guide-1000000163594-00.pdf)                                      | `--with_umi --skip_umi_extract --umitools_umi_separator ":"`                                                                                   |
+| UMI type     | Source                                                                                                                                                                                                                                              | Pipeline parameters                                                                                                                            |
+| ------------ | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------- |
+| In read name | [Illumina BCL convert >3.7.5](https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl_convert/bcl-convert-v3-7-5-software-guide-1000000163594-00.pdf)                                     | `--with_umi --skip_umi_extract --umitools_umi_separator ":"`                                                                                   |
 | In sequence  | [Lexogen QuantSeq® 3’ mRNA-Seq V2 FWD](https://www.lexogen.com/quantseq-3mrna-sequencing) + [UMI Second Strand Synthesis Module](https://faqs.lexogen.com/faq/how-can-i-add-umis-to-my-quantseq-libraries)                                          | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P<umi_1>.{6})(?P<discard_1>.{4}).*"`                                   |
 | In sequence  | [Lexogen CORALL® Total RNA-Seq V1](https://www.lexogen.com/corall-total-rna-seq/)<br> > _mind [Appendix H](https://www.lexogen.com/wp-content/uploads/2020/04/095UG190V0130_CORALL-Total-RNA-Seq_2020-03-31.pdf) regarding optional trimming_       | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P<umi_1>.{12}).*"`<br>Optional: `--clip_r2 9 --three_prime_clip_r2 12` |
 | In sequence  | [Takara Bio SMARTer® Stranded Total RNA-Seq Kit v3](https://www.takarabio.com/documents/User%20Manual/SMARTer%20Stranded%20Total%20RNA/SMARTer%20Stranded%20Total%20RNA-Seq%20Kit%20v3%20-%20Pico%20Input%20Mammalian%20User%20Manual-a_114949.pdf) | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P<umi_1>.{8})(?P<discard_1>.{6}).*"`                                  |

nextflow.config

@@ -69,7 +69,6 @@ params {
     extra_kallisto_quant_args  = null
     kallisto_quant_fraglen     = 200
     kallisto_quant_fraglen_sd  = 200
-    kallisto_quant_strandedness  = null
     save_merged_fastq          = false
     save_unaligned             = false
     save_align_intermeds       = false

nextflow_schema.json

@@ -422,13 +422,6 @@
                     "description": "Extra arguments to pass to Salmon quant command in addition to defaults defined by the pipeline.",
                     "fa_icon": "fas fa-plus"
                 },
-                "kallisto_quant_strandedness": {
-                    "type": "string",
-                    "fa_icon": "fas fa-ribbon",
-                    "description": "Override Kallisto library type inferred based on strandedness defined in meta object.",
-                    "enum": ["fr-stranded", "rf-stranded"],
-                    "help_text": "See [Kallisto docs](https://pachterlab.github.io/kallisto/manual)"
-                },
                 "extra_kallisto_quant_args": {
                     "type": "string",
                     "description": "Extra arguments to pass to Kallisto quant command in addition to defaults defined by the pipeline.",