Added stub for sratools (#5625)

* Added stub for sratools * Added command echo for fasterqdump
nf-core · May 18, 2024 · dd93531 · dd93531
1 parent 839651c
commit dd93531
Show file tree

Hide file tree

Showing 9 changed files with 255 additions and 12 deletions.
diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf
@@ -23,7 +23,10 @@ process SRATOOLS_FASTERQDUMP {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def outfile = meta.single_end ? "${prefix}.fastq" : prefix
+    def outfile = "${prefix}.fastq"
+    def exclude_third = meta.single_end ? '' : "mv $outfile $prefix || echo 'No third file'"
+    // Excludes the "${prefix}.fastq" file from output `reads` channel for paired end cases and
+    // avoids the '.' in the path bug: https://github.com/ncbi/sra-tools/issues/865
     def key_file = ''
     if (certificate.toString().endsWith('.jwt')) {
         key_file += " --perm ${certificate}"
@@ -40,6 +43,51 @@ process SRATOOLS_FASTERQDUMP {
         ${key_file} \\
         ${sra}
 
+    $exclude_third
+
+    pigz \\
+        $args2 \\
+        --no-name \\
+        --processes $task.cpus \\
+        *.fastq
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sratools: \$(fasterq-dump --version 2>&1 | grep -Eo '[0-9.]+')
+        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def outfile = "${prefix}.fastq"
+    def exclude_third = meta.single_end ? '' : "mv $outfile $prefix || echo 'No third file'"
+    // Excludes the "${prefix}.fastq" file from output `reads` channel for paired end cases and
+    // avoids the '.' in the path bug: https://github.com/ncbi/sra-tools/issues/865
+    def key_file = ''
+    if (certificate.toString().endsWith('.jwt')) {
+        key_file += " --perm ${certificate}"
+    } else if (certificate.toString().endsWith('.ngc')) {
+        key_file += " --ngc ${certificate}"
+    }
+    def touch_outfiles = meta.single_end ? "${prefix}.fastq" : "${prefix}_1.fastq ${prefix}_2.fastq"
+    """
+    touch $touch_outfiles
+
+    export NCBI_SETTINGS="\$PWD/${ncbi_settings}"
+
+    echo \\
+    "fasterq-dump \\
+        $args \\
+        --threads $task.cpus \\
+        --outfile $outfile \\
+        ${key_file} \\
+        ${sra}"
+
+    $exclude_third
+
     pigz \\
         $args2 \\
         --no-name \\

diff --git a/modules/nf-core/sratools/fasterqdump/meta.yml b/modules/nf-core/sratools/fasterqdump/meta.yml
@@ -51,3 +51,4 @@ authors:
   - "@Midnighter"
 maintainers:
   - "@Midnighter"
+  - "@gallvp"
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test
@@ -1,7 +1,6 @@
 nextflow_process {
     name "Test Process SRATOOLS_FASTERQDUMP"
     script "../main.nf"
-    config "./nextflow.config"
     process "SRATOOLS_FASTERQDUMP"
     tag "modules"
     tag "modules_nfcore"
@@ -70,4 +69,54 @@ nextflow_process {
             )
         }
     }
+
+    test("Single-end-stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_single_end', single_end:true ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/sra/SRR13255544.tar.gz', checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("Paired-end-stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_paired_end', single_end:false ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/sra/SRR11140744.tar.gz', checkIfExists: true)
+                ]
+                input[1] = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap b/modules/nf-core/sratools/fasterqdump/tests/main.nf.test.snap
@@ -30,9 +30,44 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-28T15:25:52.837288"
+        "timestamp": "2024-05-17T22:01:43.486256"
+    },
+    "Single-end-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_single_end",
+                            "single_end": true
+                        },
+                        "test_single_end.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test_single_end",
+                            "single_end": true
+                        },
+                        "test_single_end.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-17T21:40:42.335786"
     },
     "Paired-end": {
         "content": [
@@ -71,8 +106,49 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.01.0"
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-17T22:09:55.6396"
+    },
+    "Paired-end-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_paired_end",
+                            "single_end": false
+                        },
+                        [
+                            "test_paired_end_1.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_paired_end_2.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                ],
+                "reads": [
+                    [
+                        {
+                            "id": "test_paired_end",
+                            "single_end": false
+                        },
+                        [
+                            "test_paired_end_1.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e",
+                            "test_paired_end_2.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a3d61a9761e1606ef8459f0b68821d7a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
         },
-        "timestamp": "2024-02-28T15:26:42.466223"
+        "timestamp": "2024-05-17T20:35:44.782058"
     }
 }
diff --git a/modules/nf-core/sratools/fasterqdump/tests/nextflow.config b/modules/nf-core/sratools/fasterqdump/tests/nextflow.config
diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf
@@ -32,4 +32,16 @@ process SRATOOLS_PREFETCH {
     }
 
     template 'retry_with_backoff.sh'
+
+    stub:
+    """
+    mkdir $id
+    touch $id/${id}.sra
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sratools: \$(prefetch --version 2>&1 | grep -Eo '[0-9.]+')
+        curl: \$(curl --version | head -n 1 | sed 's/^curl //; s/ .*\$//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/sratools/prefetch/meta.yml b/modules/nf-core/sratools/prefetch/meta.yml
@@ -54,3 +54,4 @@ authors:
   - "@Midnighter"
 maintainers:
   - "@Midnighter"
+  - "@gallvp"
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test b/modules/nf-core/sratools/prefetch/tests/main.nf.test
@@ -46,4 +46,26 @@ nextflow_process {
             )
         }
     }
+
+    test("sratools/prefetch/stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([ [ id:'test', single_end:false ], 'DRR000774' ])
+                input[1] = file(params.modules_testdata_base_path + 'generic/config/ncbi_user_settings.mkfg', checkIfExists: true)
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll (
+            { assert process.success },
+            { assert snapshot(process.out).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap b/modules/nf-core/sratools/prefetch/tests/main.nf.test.snap
@@ -1,4 +1,43 @@
 {
+    "sratools/prefetch/stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "DRR000774.sra:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee"
+                ],
+                "sra": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        [
+                            "DRR000774.sra:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,83d1b23f5ff5b2ad1b96d17d7d7594ee"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-17T20:07:31.627115"
+    },
     "sratools/prefetch with sralite": {
         "content": [
             {
@@ -77,4 +116,4 @@
         },
         "timestamp": "2024-02-28T11:48:37.428307"
     }
-}
+}