do not snapshot the bam

nf-core · Oct 10, 2024 · 6866c24 · 6866c24
1 parent 997fb25
commit 6866c24
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Showing 9 changed files with 9 additions and 87 deletions.
diff --git a/tests/.nftignore b/tests/.nftignore
@@ -5,7 +5,7 @@ kallisto/*/kallisto_quant.log
 kallisto/*/run_info.json
 kallisto/kallisto.*
 {multiqc,multiqc/**}/multiqc_report.html
-{multiqc,multiqc/**}/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt
+{multiqc,multiqc/**}/multiqc_report_data/fastqc_{raw,trimmed}_top_overrepresented_sequences_table.txt
 {multiqc,multiqc/**}/multiqc_report_data/junction_saturation_known.txt
 {multiqc,multiqc/**}/multiqc_report_data/junction_saturation_novel.txt
 {multiqc,multiqc/**}/multiqc_report_data/kallisto_alignment.txt

diff --git a/tests/default.nf.test b/tests/default.nf.test
@@ -16,8 +16,6 @@ nextflow_pipeline {
             def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
             def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
-            // bam_files: All bam files
-            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -28,9 +26,7 @@ nextflow_pipeline {
                     // All stable path name, with a relative path
                     stable_name,
                     // All files with stable contents
-                    stable_path,
-                    // All bam files
-                    bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] }
+                    stable_path
                 ).match() }
             )
         }

diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
@@ -1299,7 +1299,6 @@
                 "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
                 "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c",
                 "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
-                "fastqc_raw_top_overrepresented_sequences_table.txt:md5,43d63c7c7f038becc6b5ef164b2e5f71",
                 "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
                 "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
                 "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
@@ -1455,28 +1454,6 @@
                 "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
                 "i_data.ctab:md5,041edee3193df311f621c09f4991892b",
                 "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe"
-            ],
-            [
-                [
-                    "RAP1_IAA_30M_REP1.markdup.sorted.bam",
-                    "289857e4f0b6c753038917027f5d88bd"
-                ],
-                [
-                    "RAP1_UNINDUCED_REP1.markdup.sorted.bam",
-                    "6c1e33dc619c8ad4799f7cf39dcf2d2f"
-                ],
-                [
-                    "RAP1_UNINDUCED_REP2.markdup.sorted.bam",
-                    "bbd70318082b935fce75ee323d5dba50"
-                ],
-                [
-                    "WT_REP1.markdup.sorted.bam",
-                    "255c653935697006430033367caa9669"
-                ],
-                [
-                    "WT_REP2.markdup.sorted.bam",
-                    "fce663681eba11bdd48c67d4281d7d4d"
-                ]
             ]
         ],
         "meta": {
@@ -1485,4 +1462,4 @@
         },
         "timestamp": "2024-10-10T09:48:14.477734"
     }
-}
+}
diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test
@@ -17,8 +17,6 @@ nextflow_pipeline {
             def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
             def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
-            // bam_files: All bam files
-            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -29,9 +27,7 @@ nextflow_pipeline {
                     // All stable path name, with a relative path
                     stable_name,
                     // All files with stable contents
-                    stable_path,
-                    // All bam files
-                    bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] }
+                    stable_path
                 ).match() }
             )
         }

diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap
@@ -1265,7 +1265,6 @@
                 "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
                 "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c",
                 "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
-                "fastqc_raw_top_overrepresented_sequences_table.txt:md5,43d63c7c7f038becc6b5ef164b2e5f71",
                 "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
                 "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
                 "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
@@ -1405,28 +1404,6 @@
                 "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
                 "i_data.ctab:md5,041edee3193df311f621c09f4991892b",
                 "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe"
-            ],
-            [
-                [
-                    "RAP1_IAA_30M_REP1.markdup.sorted.bam",
-                    "76476167553ce185faf6fa44b01d34da"
-                ],
-                [
-                    "RAP1_UNINDUCED_REP1.markdup.sorted.bam",
-                    "c3384e7240bc0291f4c6e3fb91f6cc82"
-                ],
-                [
-                    "RAP1_UNINDUCED_REP2.markdup.sorted.bam",
-                    "1db43d2a4ad9d37865e0777bf943deaf"
-                ],
-                [
-                    "WT_REP1.markdup.sorted.bam",
-                    "afa34b079825ffdcc260968053509ef3"
-                ],
-                [
-                    "WT_REP2.markdup.sorted.bam",
-                    "fd478d307f2c27138b0ff003b904c481"
-                ]
             ]
         ],
         "meta": {
@@ -1435,4 +1412,4 @@
         },
         "timestamp": "2024-10-10T10:00:00.235948"
     }
-}
+}
diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test
@@ -17,8 +17,6 @@ nextflow_pipeline {
             def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
             def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
-            // bam_files: All bam files
-            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -29,9 +27,7 @@ nextflow_pipeline {
                     // All stable path name, with a relative path
                     stable_name,
                     // All files with stable contents
-                    stable_path,
-                    // All bam files
-                    bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] }
+                    stable_path
                 ).match() }
             )
         }

diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap
@@ -761,7 +761,6 @@
                 "multiqc/hisat2/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt",
                 "multiqc/hisat2/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt",
                 "multiqc/hisat2/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt",
-                "multiqc/hisat2/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt",
                 "multiqc/hisat2/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt",
                 "multiqc/hisat2/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt",
                 "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt",
@@ -1340,4 +1339,4 @@
         },
         "timestamp": "2024-10-10T10:25:14.209047"
     }
-}
+}
diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test
@@ -17,8 +17,6 @@ nextflow_pipeline {
             def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
             // stable_path: All files in ${params.outdir}/ with stable content
             def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
-            // bam_files: All bam files
-            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -29,9 +27,7 @@ nextflow_pipeline {
                     // All stable path name, with a relative path
                     stable_name,
                     // All files with stable contents
-                    stable_path,
-                    // All bam files
-                    bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] }
+                    stable_path
                 ).match() }
             )
         }

diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap
@@ -1039,7 +1039,6 @@
                 "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82",
                 "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c",
                 "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772",
-                "fastqc_raw_top_overrepresented_sequences_table.txt:md5,43d63c7c7f038becc6b5ef164b2e5f71",
                 "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33",
                 "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6",
                 "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247",
@@ -1170,20 +1169,6 @@
                 "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b",
                 "i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e",
                 "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe"
-            ],
-            [
-                [
-                    "RAP1_IAA_30M_REP1.markdup.sorted.bam",
-                    "542a64613e641be18a172830f281b319"
-                ],
-                [
-                    "RAP1_UNINDUCED_REP1.markdup.sorted.bam",
-                    "42765cd169f11cb21c4ca680b1f8f200"
-                ],
-                [
-                    "RAP1_UNINDUCED_REP2.markdup.sorted.bam",
-                    "3146dc95e97f6b3036b046613bb5102f"
-                ]
             ]
         ],
         "meta": {
@@ -1286,4 +1271,4 @@
         },
         "timestamp": "2024-10-10T10:37:37.274627"
     }
-}
+}