add information of new tool in docs

fmalmeida · Feb 28, 2024 · a48dfd3 · a48dfd3
1 parent ceaef66
commit a48dfd3
Show file tree

Hide file tree

Showing 3 changed files with 5 additions and 1 deletion.
diff --git a/docs/index.md b/docs/index.md
@@ -23,7 +23,7 @@ The pipeline wraps up the following tools and analyses:
 
 | Software | Analysis |
 | :------- | :------- |
-|  [Canu](https://github.com/marbl/canu), [Flye](https://github.com/fenderglass/Flye), [Unicycler](https://github.com/rrwick/Unicycler), [Raven](https://github.com/lbcb-sci/raven), [Shasta](https://github.com/chanzuckerberg/shasta) and [wtdbg2](https://github.com/ruanjue/wtdbg2) | Long reads assembly |
+|  [Hifiasm](https://github.com/chhylp123/hifiasm), [Canu](https://github.com/marbl/canu), [Flye](https://github.com/fenderglass/Flye), [Unicycler](https://github.com/rrwick/Unicycler), [Raven](https://github.com/lbcb-sci/raven), [Shasta](https://github.com/chanzuckerberg/shasta) and [wtdbg2](https://github.com/ruanjue/wtdbg2) | Long reads assembly |
 | [Haslr](https://github.com/vpc-ccg/haslr), [Unicycler](https://github.com/rrwick/Unicycler) and [SPAdes](https://github.com/ablab/spades) | Hybrid assembly |
 | [Shovill](https://github.com/tseemann/shovill), [Unicycler](https://github.com/rrwick/Unicycler), [Megahit](https://github.com/voutcn/megahit) and [SPAdes](https://github.com/ablab/spades) | Short reads assembly |
 | [Nanopolish](https://github.com/jts/nanopolish), [Medaka](https://github.com/nanoporetech/medaka), [gcpp](https://github.com/PacificBiosciences/gcpp), [Polypolish](https://github.com/rrwick/Polypolish) and [Pilon](https://github.com/broadinstitute/pilon) | Assembly polishing |

diff --git a/docs/manual.md b/docs/manual.md
@@ -42,6 +42,7 @@ The pipeline is capable of assembling Illumina, ONT and Pacbio reads in three ma
     + Raven
     + Shasta
     + wtdbg2
+    + hifiasm
 
 3. **Hybrid assemblies (using both short and long reads)**
     + Unicycler
@@ -162,6 +163,8 @@ However, they can also be set in a sample-specific manner. If a sample has a val
 | `--shasta_additional_parameters`              | :material-close: | False | Passes additional parameters for Raven assembler. E.g. `" --Assembly.detangleMethod 1 "`. Must be given as shown in Shasta's manual |
 | `--skip_wtdbg2`              | :material-close: | False | Skip the execution of wtdbg2 |
 | `--wtdbg2_additional_parameters`              | :material-close: | False | Passes additional parameters for wtdbg2 assembler. E.g. `" -k 250 "`. Must be given as shown in wtdbg2's manual. Remember, the script called for wtdbg2 is `wtdbg2.pl` thus you must give the parameters used by it |
+| `--skip_hifiasm`              | :material-close: | False | Skip the execution of hifiasm |
+| `--hifiasm_additional_parameters`              | :material-close: | False | Passes additional parameters for hifiasm assembler. E.g. `" --ul ul.fq.gz "`. Must be given as shown in hifiasm's manual |
 | `--skip_unicycler`              | :material-close: | False | Skip the execution of Unicycler |
 | `--unicycler_additional_parameters`              | :material-close: | False | Passes additional parameters for Unicycler assembler. E.g. `" --mode conservative --no_correct "`. Must be given as shown in Unicycler's manual |
 | `--skip_spades`              | :material-close: | False | Skip the execution of SPAdes |

diff --git a/docs/non_bacteria.md b/docs/non_bacteria.md
@@ -38,6 +38,7 @@ nextflow run fmalmeida/mpgap \
     --skip_unicycler \
     --flye_additional_parameters ' --keep-haplotypes ' \
     --quast_additional_parameters ' --eukaryote ' \
+    --skip_hifiasm \
     --max_cpus 20 \
     --max_memory '40.GB'
 ```