update to 1.14.1

pdimens · Dec 11, 2024 · 44247a9 · 44247a9
1 parent c001d6a
commit 44247a9
Showing 1 changed file with 19 additions and 10 deletions.
diff --git a/Workflows/other.md b/Workflows/other.md
@@ -1,15 +1,13 @@
 ---
 label: Other
-icon: file-diff
+icon: ellipsis
 description: Generate extra files for analysis with Harpy
 order: 7
 ---
 
-# :icon-file-diff: Other Harpy modules
-On this page you'll find Harpy functions that aren't standalone workflows. These may create ancillary inputs, continue where you left off,
-view important workflow files, etc.
+# :icon-ellipsis: Other Harpy modules
+On this page you'll find Harpy functions that do other, ancillary things.
 
-## :icon-terminal: Other modules
 {.compact}
 | module         | description                                                                      |
 | :------------- | :------------------------------------------------------------------------------- |
@@ -24,15 +22,26 @@ view important workflow files, etc.
 ### downsample
 While downsampling (subsampling) FASTQ and BAM files is relatively simple with tools such as `awk`, `samtools`, `seqtk`, `seqkit`, etc.,
 Harpy offers the `downsample` module, which allows you to downsample a BAM file (or paired-end FASTQ) _by barcodes_. That means you can
-keep all the reads associated with `d` number of barcodes.
+keep all the reads associated with `d` number of barcodes. First, barcodes are extracted, then subsampled, then the reads associated
+with those barcodes are extracted. The `--invalid` proportion will determine what proportion of invalid barcodes appear in the barcode
+pool that gets subsampled, where `0` is none, `1` is all invalid barcodes, and a number in between is that proportion, e.g. `0.5` is half.
+Bear in mind that the barcode pool still gets subsampled, so the `--invalid` proportion doesn't necessarily reflect how many end up getting
+sampled, rather what proportion will be considered for sampling. 
+
+!!! Barcode tag
+Barcodes must be in the `BX:Z` SAM tag for both BAM and FASTQ inputs. See [Section 1 of the SAM Spec here](https://samtools.github.io/hts-specs/SAMtags.pdf).
+!!!
 
 ```bash usage
-# a BAM file
 harpy downsample OPTIONS... INPUT(S)...
 ```
 
 ```bash example
-harpy downsample -d 1000 -i drop -b BC -p sample1.sub1000
+# BAM file
+harpy downsample -d 1000 -i 0.3 -p sample1.sub1000 sample1.bam
+
+# FASTQ file
+harpy downsample -d 1000 -i 0 -p sample1.sub1000 sample1.F.fq.gz sample1.R.fq.gz
 ```
 
 #### arguments
@@ -41,10 +50,10 @@ harpy downsample -d 1000 -i drop -b BC -p sample1.sub1000
 | :-------------- | :--------: | :-----------: | :-------------------------------------------------------------------------------------------------------------------------------- |
 | `INPUT(S)`      |            |               | [!badge variant="info" text="required"] One BAM file or both read files from a paired-end FASTQ pair                              |
 | `--downsample`  |    `-d`    |               | [!badge variant="info" text="required"] Number of barcodes to downsample to                                                       |
-| `--invalid`     |    `-i`    |    `keep`     | Strategy to handle invalid/missing barcodes [`keep`,`drop`]                                                                       |
-| `--bx-tag`      |    `-b`    |     `BX`      | The header tag with the barcode [!badge variant="secondary" text="alphanumeric"] [!badge variant="secondary" text="2 characters"] |
+| `--invalid`     |    `-i`    |       1       | Proportion of barcodes to sample                                                                                                  |
 | `--prefix`      |    `-p`    | `downsampled` | Prefix for output files                                                                                                           |
 | `--random-seed` |            |               | Random seed for sampling [!badge variant="secondary" text="optional"]                                                             |
+| `--snakemake`   |            |               | Additional Snakemake arguments, in quotes                                                                                         |
 | `--threads`     |    `-t`    |      `4`      | Number of threads to use                                                                                                          |
 | `--quiet`       |            |               | Don't show output text while running                                                                                              |