Merge pull request #3 from tkchafin/pacbio_fastq

Pacbio fastq
tkchafin · Aug 14, 2024 · 4c39fe6 · 4c39fe6
2 parents eb95288 + e2a8d46
commit 4c39fe6
Show file tree

Hide file tree

Showing 17 changed files with 522 additions and 16 deletions.
diff --git a/assets/samplesheet_s3.csv b/assets/samplesheet_s3.csv
@@ -4,4 +4,4 @@ mMelMel2,illumina,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_d
 mMelMel3,hic,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/hic/35528_2%231.subset.cram,
 mMelMel3,ont,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/ont/PAE35587_pass_1f1f0707_115.subset.fastq.gz,
 mMelMel3,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200910_173211.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.bam,
-mMelMel3,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.bam,
+mMelMel3,pacbio,https://tolit.cog.sanger.ac.uk/test-data/Meles_meles/genomic_data/mMelMel3/pacbio/m64094_200911_174739.ccs.bc1022_BAK8B_OA--bc1022_BAK8B_OA.subset.fastq.gz,
diff --git a/docs/usage.md b/docs/usage.md
@@ -42,7 +42,7 @@ sample1_T5,pacbio,pacbio2.bam,pacbio2
 | ---------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `sample`   | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (\_).                                                 |
 | `datatype` | Type of sequencing data. Must be one of `hic`, `Illumina`, `pacbio`, or `ont`.                                                                                                                                                        |
-| `datafile` | Full path to read data file. Must be `bam` or `cram` or `fastq.gz` or `fq.gz` for `Illumina` and `HiC`. Must be `bam` for `pacbio`. Must be `fastq.gz` or `fq.gz` for `ont`.                                                          |
+| `datafile` | Full path to read data file. Must be `bam`, `cram`, `fastq.gz` or `fq.gz` for `Illumina` and `HiC`. Must be `bam`, `fastq.gz` or `fq.gz` for `pacbio`. Must be `fastq.gz` or `fq.gz` for `ont`.                                       |
 | `library`  | (Optional) The library value is a unique identifier which is assigned to read group (`@RG`) ID. If the library name is not specified, the pipeline will auto-create library name using the data filename provided in the samplesheet. |
 
 An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.

diff --git a/modules.json b/modules.json
@@ -86,6 +86,16 @@
                         "git_sha": "6c2309aaec566c0d44a6cf14d4b2d0c51afe2e91",
                         "installed_by": ["modules"]
                     },
+                    "seqkit/fq2fa": {
+                        "branch": "master",
+                        "git_sha": "03fbf6c89e551bd8d77f3b751fb5c955f75b34c5",
+                        "installed_by": ["modules"]
+                    },
+                    "seqtk/subseq": {
+                        "branch": "master",
+                        "git_sha": "730f3aee80d5f8d0b5fc532202ac59361414d006",
+                        "installed_by": ["modules"]
+                    },
                     "untar": {
                         "branch": "master",
                         "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",

diff --git a/modules/nf-core/seqkit/fq2fa/environment.yml b/modules/nf-core/seqkit/fq2fa/environment.yml
diff --git a/modules/nf-core/seqkit/fq2fa/main.nf b/modules/nf-core/seqkit/fq2fa/main.nf
diff --git a/modules/nf-core/seqkit/fq2fa/meta.yml b/modules/nf-core/seqkit/fq2fa/meta.yml
diff --git a/modules/nf-core/seqkit/fq2fa/tests/main.nf.test b/modules/nf-core/seqkit/fq2fa/tests/main.nf.test
diff --git a/modules/nf-core/seqkit/fq2fa/tests/main.nf.test.snap b/modules/nf-core/seqkit/fq2fa/tests/main.nf.test.snap
diff --git a/modules/nf-core/seqkit/fq2fa/tests/tags.yml b/modules/nf-core/seqkit/fq2fa/tests/tags.yml
diff --git a/modules/nf-core/seqtk/subseq/environment.yml b/modules/nf-core/seqtk/subseq/environment.yml
diff --git a/modules/nf-core/seqtk/subseq/main.nf b/modules/nf-core/seqtk/subseq/main.nf
diff --git a/modules/nf-core/seqtk/subseq/meta.yml b/modules/nf-core/seqtk/subseq/meta.yml